This research was to examine the impacts of long-term integrated rice–crayfish farming on soil nutrients, carbon pools, and rice yields in paddy fields. The aim was to establish a scientific basis for the sustainable development of RS in the northern region of Zhejiang. The results showed that the change from rice monoculture (CK) to rice–crayfish coculture systems (RS) led to a 24.99% increase in the 5-year average of soil ammonium nitrogen (AN), while the soil nitrate nitrogen (NN), available potassium (AK), and available phosphorus content (AP) decreased by 28.02%, 16.05%, and 28.76%, respectively. Moreover, the total organic carbon (TOC), easily oxidizable organic carbon (EOC), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) exhibited a reduction of 2.45%, 8.82%, 35.31%, and 65.84%, respectively. Correlation analysis revealed a significant positive correlation between NN, EOC, and MBC in the RS mode. In terms of rice yield, the 5-year average of rice yield in RS decreased by 8.40% compared to CK. The mean yield of early-maturing rice varieties was reduced by 13.16%, while that of late-maturing rice varieties was reduced by 6.00%. These results shed light on the annual variation in soil nutrients, carbon pools, and rice yield in the RS mode, providing insights for the sustainable development of RS in northern Zhejiang.