Rice‐crayfish (RC) integrated cultivation, as a sustainable agricultural system, could significantly improve soil fertility. However, the soil quality under the long‐term RC farming system is still unclear. To examine the effects of RC cultivation on soil quality in paddy fields, this study utilized an integrated soil quality index (SQI) for examining the soil quality at different soil profiles (0–10, 10–20, and 20–30 cm depth) in rice monoculture (RM) and RC farming systems (after 1, 6, 10, and 15 years) scattered in Nanxian County, Hunan Province, China. The minimum datasets for evaluating soil quality were assembled using the soil pH, bulk density, total nitrogen, microbial biomass carbon, microbial biomass nitrogen, and β‐d‐glucosidase. The findings demonstrated that soil quality was greatly impacted by RC farming, which improved with the increase of years under RC management. The soil quality of 10‐ and 15‐year RC farming systems were significantly higher than RM system. Besides, soil quality declined with increasing soil depth. The SQI value, which may be used as an indicator to assess the soil quality of RC systems, was dominated by total nitrogen, which contributed 27.60% to the SQI value. On the whole, long‐term RC farming affected the soil quality of paddy fields through management methods including non‐rice season flooding, feeding, and no tillage. Through this study, it was found that MDS and SQI composed of appropriate physical, chemical, and biological indicators could more objectively analyze the soil quality of long‐term RC system and provide guidance for sustainable development of RC farming.