Purpose: Soil organic matter (SOM) is essential for crop production and serves as a critical indicator for soil fertility. A large deal of research has shown a large increase in the SOM content of rice fields in southern China. However, the responses of rice yield and fertilizer nitrogen (N) fate to the increased SOM remain unclear. The objective of the present study is to investigate the responses of rice yield and N use efficiency to SOM in a double-cropped rice system in subtropical China. Methods: A 2-year field experiment was conducted on three paddy fields with low, medium, and high SOM content (corresponding to a SOM concentration of 20.3, 28.5, and 37.7 g kg(- 1), respectively) to examine the responses of rice yield and N uptake to SOM. Meanwhile, N-15-labelled micro-plot experiments were carried out to clarify fertilizer N recovery efficiency, N residual in soil, and N losses to environment as affected by SOM. Results: Overall, our results showed that compared to low SOM, medium and high SOM increased rice yield by 5.4% and 19.9%, respectively. Compared to low SOM, medium and high SOM increased N-15 residues in soil by 51.6% and 90.7%, and reduced N-15 losses to the environment by 23.6% and 40.0%, respectively. We found a stronger response of grain yield and N-15 recovery efficiency to SOM for late rice than for early rice. Compared to low SOM, medium and high SOM enhanced early rice yield by 5.0% and 17.2%, whereas the increase was 5.9% and 22.2% for late rice yield, respectively. Relative to low SOM, medium and high SOM increased the N-15 recovery efficiency of late rice by 14.5% and 28.6%, respectively, but did not affect that of early rice. Conclusions: The present results demonstrate that increasing SOM can not only enhance rice yield but also improve fertilizer N retention and reduce fertilizer N losses in the double-cropped rice field. Furthermore, we suggest that fertilizer N management should take into account the different response of early and late rice to SOM.