The sustainable development of the aquaculture industry is of great significance for national food security within the context of increasing consumer demand, scarce land resources, and continuous ecological and environmental deterioration. China is a major shrimp farming country. It is crucial to investigate the spatiotemporal variations in the characteristics of shrimp aquaculture for the stability and sustainable development of China’s shrimp aquaculture industry, as well as to explore an optimization strategy for the spatial layout of this industry. Existing research mainly focuses on the fluctuations in shrimp production and their influencing factors, while studies on the spatiotemporal variations of shrimp aquaculture and their influencing mechanisms are few. In this study, we analyzed the patterns of spatiotemporal variation in shrimp aquaculture in China and further explored their influencing factors using standard deviational ellipse and Geodetector, based on China’s shrimp aquaculture production data from 2003 to 2020. The results show that (1) there has been a steady upward trend in shrimp aquaculture production in China over the past 18 years, with a growth rate of 128% and an average annual growth rate of 5.2%; (2) the spatial distribution range of shrimp farms has expanded, showing a zonal distribution pattern from the northeast to southwest, and the center of the shrimp aquaculture industry has generally shifted southward; and (3) the level of development within the fishing industry, labor quantity, and per capita income are the main factors affecting the spatial distribution variability of shrimp aquaculture. The degree of influence of each different factor on spatial distribution of shrimp aquaculture varied temporally.