The rice–crayfish rotation system (RCR), originating in the Jianghan Plain, is developing rapidly in various regions of China and has been characterized by unbalanced regional development, which has also led to widespread concerns and discussion on its environmental impacts and sustainability. This study selects representative RCR production areas in the Jianghan Plain, including Jianli, Qianjiang, Shishou, Shayang, Gong’an and Honghu, to analyze resource inputs, resource utilization efficiency, environmental impacts and sustainability by employing the emergy analysis method. Our analysis of Jianli, Honghu, Qianjiang, Gong’an, Shishou and Shayang reports total emergy inputs ranging from 6.46 × 1016 to 8.25 × 1016, with renewable rates between 78.38% and 84.34%. Shishou leads in the unit emergy value (5.58 × 10−1) and the emergy yield ratio (5.30). The sustainability evaluation finds that the environmental loading ratio is from 0.19 to 0.28 and the emergy index for sustainable development varies between 1.27 and 3.00. This analysis indicates that the southern regions have higher inputs and efficiency, with southeastern areas showing lower environmental impact and higher sustainability. We also underscore the impact of non-renewable resources on environmental outcomes and sustainability, suggesting tailored development strategies for the rice–crayfish rotation system’s optimization and sustainable growth.