With the rapid development of aquaculture in China in recent decades, the country now faces environmental problems, such as high energy consumption and severe environmental pollution. The Yangtze River Basin is the most important area for freshwater aquaculture production in China, accounting for more than half of the total production. The environmental issues induced by aquaculture have received widespread consideration in this area. However, the freshwater farming-induced environmental issues in the Yangtze River Basin were rarely evaluated in prior research. Life cycle assessment (LCA) is a valid tool for assessing environmental impacts and resources and is widely deployed in the industrial sector. It can quantify the impact of a product or service on different environmental indicators at various stages of the production process, thereby aiding in the identification of the best measures to reduce environmental impacts. The LCA is more effective than traditional environmental impact assessment methods; thus, it has been gradually applied in other fields, such as agriculture and aquaculture, in recent years. In aquaculture, LCA has been used to evaluate the environmental impact of various farming models or species in a laboratory setting. However, little attention has been paid to large-scale systems, such as the Yangtze River Basin. The two most important farming models in China are the pond farming model and the integrated rice-fish farming model. Among them, the integrated rice-fish farming model is regarded as environmentally friendly and an important step towards realizing the sustainable development of aquaculture in terms of the efficient utilization of water and land resources. Therefore, in this study, the environmental effects of pond farming and integrated rice-fish farming models were investigated in the Yangtze River Basin using the LCA method. A total of 20 monitoring points were established in the Yangtze River Basin, including 5 for integrated rice-fish farming and 15 for pond culture. In the integrated rice-fish farming model, the life cycle consists of two stages: Feed supply and breeding. In pond culture, the life cycle consists of three stages: Feed supply, power supply, and breeding. We analyzed the values of energy use (EU), global warming potential (GWP), acidification potential (AP), eutrophication potential (EP), and water use (WU) in the pond farming and integrated rice-fish farming models using the LCA method, assessed the contribution rate of each phase for environmental indices, and compared the environmental impact of the two farming models. In order to establish the inputs and outputs of an aquaculture system, experimental measurements and surveys were conducted to collect data. The collected data mainly included feed consumption, electricity consumption, water consumption, total phosphorus and total nitrogen emissions, and greenhouse gas (CH4 and N2O) emissions. The data were analyzed by the LCA software eBalance. In this study, the weight gain of 1 ton of aquaculture products served as the functional unit, and the results were standardized and evaluated in order to compare the environmental impacts of various impact indicators. The results showed that the standardized and weighted evaluation values of WU, EP, GWP, AP, and EU in the integrated rice-fish farming model were 11.650, 0.770, 0.141, 0.096, and 0.003, respectively, and the total environmental impact indicator was 12.660. In the pond farming model, the values of WU, EP, GWP, AP, and EU were 31.453, 1.187, 0.210, 0.174, and 0.007, respectively, and the total environmental impact indicator was 33.031. The environmental impacts of integrated rice-fish farming were lower than those of pond farming. The contribution rate analysis of the three stages of the life cycle to environmental impact showed that the contribution rates of EU, GWP, and AP in the feed supply stage were higher than those in the power supply and breeding stages. EP was primarily associated with the feed supply stage and pollutant discharge stages of the breeding process, and WU was principally concentrated on the breeding stage. Overall, the LCA results showed that the integrated rice-fish farming model had a more environmentally friendly effect than the pond farming model, which indicates that the Yangtze River Basin has considerable development potential. WU was the most influential environmental impact indicator and the main restriction factor in aquaculture; it was mainly associated with the breeding stage. Therefore, moderately increasing stocking density was an effective strategy for reducing water resource consumption and improving water resource utilization rates. In addition to WU, the main environmental impact index of the pond culture model and integrated rice-fish farming models comprised EP, followed by GWP, AP, and EU. The contribution rate analyses of the two models showed that the aquaculture-induced environmental impacts could be mitigated by improving feed production technology, establishing accurate feeding technologies, applying advanced effluent water treatment technologies, and appropriately increasing stocking density in the Yangtze River Basin. In summary, in this study, we compared the environmental impacts between the pond culture and integrated rice-fish farming models in the Yangtze River Basin using the LCA method. In addition, we analyzed the differences between environmental impacts at different production stages. These data served as a reference for the sustainable development and optimization of aquaculture in the Yangtze River Basin.