The rice–crayfish co-culture system, a representative of Agri-aqua food systems, has emerged worldwide as an effective strategy for enhancing agricultural land use efficiency and boosting sustainability, particularly in China and Southeast Asia. Despite its widespread adoption in China’s Jianghan Plain, the exact spatiotemporal dynamics and factors influencing this practice in this region are yet to be clarified. Therefore, understanding the spatiotemporal dynamics and influencing factors of the rice–crayfish fields (RCFs) is crucial for promoting the rice–crayfish co-culture system, and optimizing land use policies. In this study, we identified the spatial distribution of RCF using Sentinel-2 images and land use spatiotemporal data to analyze its spatiotemporal dynamics during the period of 2016–2020. Additionally, we used the Multiscale Geographically Weighted Regression model to explore the key factors influencing RCF’s spatiotemporal changes. Our findings reveal that (1). the RCF area in Jianghan Plain expanded from 1216.04 km2 to 2429.76 km2 between 2016 and 2020, marking a 99.81% increase. (2). RCF in Jianghan Plain evolved toward a more contiguous and clustered spatial pattern, suggesting a clear industrial agglomeration in this area. (3). The expansion of the RCFs was majorly influenced by its landscape and local agricultural conditions. Significantly, the Aggregation and Landscape Shape Indexes positively impacted this expansion, whereas proximity to rural areas and towns had a negative impact. This study provides a solid foundation for promoting the rice–crayfish co-culture system and sustainably developing related industries. To ensure the sustainable development of rice–crayfish co-culture industries in Jianghan Plain, we recommend that local governments optimize the spatial layout of rural settlements, improve transportation infrastructure, and enhance regional agricultural water sources and irrigation system construction, all in line with the national strategy of rural revitalization and village planning. Additionally, promoting the concentration and contiguity of RCF through land consolidation can achieve efficient development of these industries.