This study was designed to explore changes in soil bulk density (BD), soil organic carbon (SOC) content, SOC stocks, and soil labile organic carbon (C) fractions after 5 years of soil tillage management under the double-cropping rice system in southern of China. The experiment included four soil tillage treatments: rotary tillage with all crop residues removed as a control (RTO); conventional tillage with crop residues incorporation (CT); rotary tillage with crop residues incorporation (RT); and no-tillage with crop residues retention. Our results revealed that soil tillage combined with crop residue incorporation (CT and RT) significantly decreased BD at 0–20 cm soil layer compared to RTO treatment. SOC content and stocks were increased with the application of crop residues. Compared with RTO treatment, SOC content and stocks were increased by 16.8% and 9.8% in CT treatment, respectively. Soil non-labile C content and proportion of labile C were increased due to crop residue incorporation. Compared with RTO treatment, soil proportion of C mineralisation (Cmin), permanganate oxidisable C (KMnO4), particulate organic C (POC), and microbial biomass C (MBC) was increased by 196.1%, 41.4%, 31.4%, and 17.1% under CT treatment, respectively. These results were confirmed by the carbon management index, which was significantly increased under soil tillage with crop residue incorporation. Here, we demonstrated that soil tillage and crop residue incorporation can increase the pool of stable C at surface soil layer while increasing labile C content and proportion. In conclusion, conventional or rotary tillage combined with crop residue incorporation is a soil management able to improve nutrient cycling and soil quality in paddy fields in southern China.