Increasing soil carbon (C) sequestration in paddy field and improving rice nitrogen use efficiency (NUE) are vital for sustainable agriculture and environmental protection. It was a benefit practice for achieving these goals by taken rice straw and organic manure managements. However, there is still need to further investigate the effects of different long-term fertilizer managements on soil C sequestration and NUE under the double-cropping rice system in southern of China. Therefore, the effects of different long-term (36-years) fertilizer practices on soil C sequestration and NUE under the double-cropping rice system in southern of China were investigated in the present paper. The field experiment was included four different fertilizer treatments: chemical fertilizer alone (MF), rice straw residue and chemical fertilizer (RF), 30% organic manure and 70% chemical fertilizer (OM), and without fertilizer input as a control (CK). This result indicated that soil C content at plough layer in paddy field with RF and OM treatments were increased, compared with MF and CK treatments. Besides input C directly into paddy field, soil original organic C accumulation with RF and OM treatments were increased by 1.54% and 3.01%, compared with MF treatment. This result indicated that soil TOC content increase rate and annual topsoil organic C sequestration rate in paddy field with RF and OM treatments increased by 55.56%, 88.89% and 48.05%, 76.62%, compared with MF treatment, respectively. Compared with MF treatment, NUE with RF and OM treatments increased by 10.43% and 22.61%, respectively, mainly due to increasing soil organic C. Grain yield of double-cropping rice with RF and OM treatments increased by 1009.5 and 1166.5 kg ha−1, compared with MF treatment, respectively. This result indicated that there was significantly correlation between NUE/NUENPK and TOC content with RF and OM treatments, at early rice and late rice growth seasons. Therefore, it was benefit practice for increasing soil carbon sequestration and improving rice NUE in the double-cropping rice system with long-term application of rice straw and organic manure managements.