Objective To investigate the changes in the organic carbon pool and stoichiometric ratios under a long-term low-input rice-fish co-culture system, deeply analyze the carbon pool dynamics in the rice-fish system, and enhance its ecological functions.

Method The study focused on the long-term low-input rice-fish co-culture system in Chenxi County, a representative county of traditional rice-fish co-culture in Hunan, China. The changes in nutrient storage within the rice-fish co-culture systems, which have been in operation for 15 years (FR15) and 50 years (FR50), were analyzed, and the key influencing factors were explored.

Result Compared to rice monoculture (MR), FR15 showed significant reductions in soil organic carbon/total nitrogen/total phosphorus/nitrate nitrogen/ammonium nitrogen/available phosphorus contents, organic carbon storage/nitrogen storage/phosphorus storage, readily oxidized organic carbon content and its proportion in organic carbon. The C∶N, pH, particulate organic carbon content and its proportion, mineral-associated organic carboncontent proportion, carbon pool activity, and carbon pool activity index increased significantly by 47.98%, 13.15%, 35.47%, 72.24%, 31.68%, 58.07%, and 58.07%, respectively. FR50 experienced significant increases in total nitrogen content, C∶P, N∶P, and nitrate nitrogen content by 13.13%, 33.08%, 14.31%, and 51.52%, respectively, while total phosphorus content, volume weight, organic carbon storage, phosphorus storage, readily oxidized organic carbon content, mineral-associated organic carbon content and its proportion decreased significantly.

Conclusion Although the low-input rice-fish co-culture system may lead to nutrient loss, the extended self-maintenance of the system enables it to recover nutrient storage autonomously. The findings provide a theoretical basis for optimizing the rice-fish co-culture system, which could help enhance its ecological functions and sustainability.