China is currently entering a stage of high-quality development, with urban development and governance facing systematic reconstruction of internal and external conditions, showing clear differences and the complex superposition of multi-stage development. The steady progress of urbanization has facilitated significant changes in the population structure of Chinese cities. It is expected that the population and industries will further converge to urban agglomerations and big cities, indicating basic multicenter and network patterns. Therefore, analyzing the negative population growth risks of urban agglomerations at different development stages is crucial. This study examined the cities of 19 urban agglomerations in China by adopting the data of the seventh population census, employing the optimized fuzzy logic method, building a complex network of population flow with ArcGIS and MATLAB platforms, and using the intensity of population flow and the registered population fertility rate to represent exogenous and endogenous growth, respectively. The negative population growth evaluation index system was constructed with five indicators: child ratio, aging rate, average family size, population density, and sex ratio. The risk index of negative population growth was measured using the fuzzy logic method, and the growth mechanism of negative population growth risk in urban agglomerations in China was analyzed using the spatial measurement method. (1) The negative population growth risk of growing urban agglomerations was influenced by both exogenous and endogenous growth, with exogenous growth having a greater impact. (2) The dynamic mechanism of negative population growth risk in large urban agglomerations is exogenous growth, whereas that of nurturing urban agglomerations is endogenous growth. (3) According to the risk of negative population growth in China's urban agglomerations and its influencing factors, negative population growth in 19 urban agglomerations can be divided into eight types. 1) The state of population growth of expanding urban agglomerations can be divided into two types, with the middle reaches of the Yangtze River and Chengdu-Chongqing urban agglomerations as one type; the capital city has a low risk of negative population growth, while other cities have a high risk of negative population growth. The Yangtze River Delta, Pearl River Delta, and Beijing-Tianjin-Hebei city clusters are the same, with the capital and other cities having a relatively low risk of negative population growth. 2) The status of large urban agglomerations can be divided into two types: Shandong Peninsula, Central Plains, Guanzhong Plain, and Beibu Gulf urban agglomerations. The capital city has a low risk of negative population growth, whereas other cities have a high risk of negative population growth. The risk of negative population growth in capital cities and other cities is relatively low. 3) The state of population growth of cultivated urban agglomerations can be divided into four types: the Harbin and Changsha urban agglomerations and the central and southern Liaoning urban agglomerations, which have a high risk of negative population growth. Meanwhile, the northern slope of the Tianshan Mountain City cluster and the Hubao Eyu City cluster have low risk of negative population growth. The risk of negative population growth is low in the provincial capital city and high in the other cities, while endogenous growth is positive in the provincial capital city and negative in the other cities. In the Jinzhong City, Central Guizhou City, and Central Yunnan City groups, the risk of negative population growth is low in provincial cities and high in other cities. Endogenous growth shows that the capital city and other cities have positive growth. In conclusion, this study posits that upgrading urban agglomerations should consider the spatial balance of population distribution, large urban agglomerations should fulfill their role in "blocking the flow" of big cities, and nurturing urban agglomerations should "consolidate human capital." This study presents a comprehensive and in-depth analysis of the negative population growth risk and its impact mechanisms in different development stages of urban agglomerations. This can provide a decision-making reference for the formulation of scientific and reasonable population and economic policies in various urban agglomerations and plays a significant role for maintaining a long-term stable population, economy, and social growth in the region.