Objectives Rice-crayfish farming is a well-advised practice for efficient rice production and soil fertility maintenance. We studied the change of the soil organic carbon pool and some enzyme activities caused by the practice, for further understanding the mechanism of fertility improvement.

Methods Rice-crayfish farming (CR) experiment had been conducted for 10 consecutive years (2005–2015), with single rice planting (MR) as control. The soil samples were collected in soil layers of 0–10 cm, 10–20 cm, 20–30 cm, 30–40 cm after rice harvesting in mid-October 2015. The contents of total organic carbon (TOC), microbial biomass carbon (MBC), dissolved organic carbon (DOC), easily-oxidized organic carbon (EOC) and particulate organic carbon (POC) were analyzed. The contents of organic carbon in the soil water-stable aggregates were determined, and the soil carbon pool management index (CPMI) was calculated. The soil cellulase, sucrase, urease and acid phosphatase activities which waere closely related to soil carbon, nitrogen and phosphorus metabolism were also analyzed.

Results 1) Compared with the rice monoculture, the rice-crayfish farming significantly increased the contents of TOC, POC and DOC in the 0–40 cm soil layer, significantly increased the content of MBC in the 30–40 cm soil layer, and significantly increased the content of EOC in the 10–40 cm soil layer. 2) The rice-crayfish farming significantly improved the soil carbon pool management index in the soil layer of 10–30 cm, with increase rate of 52.7% and 58.2% in the soil layer of 10–20 cm and 20–30 cm, compared with the rice monoculture, respectively. 3) The rice-crayfish farming significantly increased the organic carbon contents of < 0.053 mm silt-clay aggregate in the 0–20 cm soil layer, and those of all the particle size of aggregates in the 20–30 cm soil layer. 4) The urease activity in the 10–20 cm soil layer of the CR system was significantly decreased by 16.7%, while the cellulase activity in the 20–30 cm soil layer was significantly increased by 28.0%, compared with the rice monoculture. 5) Except DOC, the contents of TOC, POC and MBC were significantly and positively correlated with the activities of cellulase, sucrase, urease and acid phosphatase.

Conclusions The long-term rice-crayfish co-culture could significantly increase the contents of soil organic carbon and the active organic carbon components, increase the organic carbon contents in all sizes of water stable aggregates and soil cellulose enzyme activities in 20–30 cm soil layer, which is beneficial to the improvement of soil texture, deep growth of rice root and maintenance of available nutrients, consequently improve the soil biological fertility of paddy fields.