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● Agricultural intensification reduced the complexity and connectance of soil food webs. ● Agricultural intensification impaired the robustness of pollination networks. ● High connectance in co-occurrence networks indicates efficient nutrient utilization. Complex network theory has been increasingly used in various research areas, including agroecosystems. This paper summarizes the basic concepts and approaches commonly used in complex network theory, and then reviews recent studies on the applications in agroecosystems of three types of common ecological networks, i.e., food webs, pollination networks and microbial co-occurrence networks. In general, agricultural intensification is considered to be a key driver of the change of agroecosystems. It causes the simplification of landscape, leads to the loss of biocontrol through cascading effect in food webs, and also reduces the complexity and connectance of soil food webs. For pollination networks, agricultural intensification impaired the robustness by reducing specialization and enhancing generality. The microbial co-occurrence networks with high connectance and low modularity generally corresponded to high efficiency in utilization of nutrients, and high resistance to crop pathogens. This review aims to show the readers the advances of ecological networks in agroecosystems and inspire the researchers to conduct their studies in a new network perspective.