Objectives This study investigated the synergistic effects of partial substitution of chemical fertilizers with organic fertilizers at different ratios on soil carbon sequestration and crop yield, aiming to propose an optimum ratio used in the rice-wheat rotation system.

Methods A two-year field experiment was carried out in a rice-wheat rotation system in Suizhou, Hubei Province. A total of 11 treatments were set up, including: no fertilization control, farmers’ habitual fertilization, recommended fertilization (RF), and RF without N fertilizer, without P fertilizer, with 6 organic substitution ratios from 10% to 100% (RFM10, RFM20, RFM30, RFM40, RFM50, M100). Soil and plant samples were collected during the harvesting period of the rice and wheat, and the components of soil active and passive carbon pools, crop yield, and indexes for nitrogen use efficiencies were measured and analyzed.

Results 1) Compared with RF, all the organic substitution treatments, except RFM10, significantly increased soil organic carbon, total N and available P by 12.8%−35.7%, 3.4%−19.6%, and 21.2%−195.4%, respectively, and enhanced soil pH by an average of 0.22 units. 2) RFM30 and M100 treatments demonstrated the highest passive carbon pool, which as 30.9% and 41.0% higher than RF did. More than 40% of organic substitution increased the soil liability index by 4.9% and 7.8%, and the soil carbon pool management index by 23.1% and 21.8% in rice and wheat seasons, respectively, relative to those of RF. The carbon sequestration index among the 6 organic substitution treatments was similar in the rice season, while that of RFM30 treatment in the wheat season was significantly higher than those of the other treatments, except for the RFM10 treatment. 3) With the increasing of organic substitution ratio, the crop yields and nitrogen use efficiency showed a trend of first rising and then falling, peaking in RFM30 with the increase of crop yields by 6.28% and nitrogen agronomic use efficiency by 74.91%, compared to RF. 4) The results of correlation and partial least squares path modeling analysis revealed that the soil passive carbon pool correlated closer with crop yield than the active carbon pool; that is, the higher content of the passive carbon pool, the higher crop yield.

Conclusions On the basis of recommended fertilization, substitution of part of the chemical fertilizer by organic fertilizers could realize the multiple targets of improving soil nutrient supply, enhancing the carbon sequestration of soil, and increasing crop yields and nitrogen utilization efficiency. The organic substitution ratio of 30% shows the highest comprehensive effectiveness, therefore, it is recommended in the rice-wheat rotation system in the middle and lower reaches of the Yangtze River.