Changes in soil bulk density (BD), soil organic carbon (SOC) content, SOC stocks and soil labile organic C fractions (mineralizable C (Cmin), microbial biomass C (MBC), dissolved organic C (DOC), particulate organic C (POC), light fraction organic C (LFOC) and permanganate oxidizable C (KMnO4-C)) were explored over 3 years in a double-cropping rice system of southern China. Five organic and inorganic nitrogen (N) inputs were used: (1) 100% from chemical fertilizer (M0), (2) 30% from organic manure, 70% from chemical fertilizer (M30), (3) 50% from organic manure, 50% from chemical fertilizer (M50), (4) 100% from organic manure (M100) and (5) without N fertilizer input, as control (CK). All organic manure treatments decreased BD significantly in the 0–20 cm soil layer compared with CK. The SOC content and stocks with organic manure were significantly higher than in M0 or CK; also, the cumulative amount of SOC stocks in M30 and M50 increased at the plough layer, compared with CK. The non-labile C content increased significantly and the percentage of labile C were significantly higher with organic manure application than in M0 or CK. The soil carbon management index (CMI) also increased significantly under the application of organic manure. Therefore, application of organic manure can increase the pool of stable C in surface layers, and increase content and percentage of labile C. Based on soil carbon storage and CMI, the combined application of 30 or 50% N of organic manure with chemical fertilizer improves carbon cycling services and soil quality in southern China paddy soil.