The partial substitution of chemical nitrogen (N) fertilizer with organic fertilizers is widely used to maintain soil fertility and enhance crop yield, although its effects on soil organic carbon (SOC) composition, mineralization and stability are not fully understood. For this study, a 12-year field experiment was conducted in a rubber plantation field of Hainan Island, China. Three fertilizer treatments included no fertilizer application as control (CK), chemical fertilizer application (NPK), and half of the chemical N fertilizer plus manure application equivalent to half of chemical N fertilizer (NPKM). We determined the soil physicochemical properties, four labile SOC compositions (microbial biomass carbon (MBC), light fraction organic carbon (LFOC), dissolved organic carbon, dissolved organic carbon extracted by hot water (HOC), particulate organic carbon (POC)), four C-associated soil enzymes (β-1, 4-glucosidase (BG), polyphenol oxidase (POX), catalase (CAT) and cellulase), and SOC mineralization (from a 46-day aerobic incubation experiment) in two soil layers (topsoil layer (0–10 cm) and subsoil layer (10–20 cm)). Compared with NPK, NPKM significantly increased soil pH, total nitrogen, total phosphorus, available phosphorus and potassium, NH4+-N, and NO3−-N contents, and SOC, LFOC, POC, HOC, and MBC concentrations. NPKM had higher cumulative CO2 production but lower SOC mineralization potential (Cp) than NPK, although the difference was not significant. In both soil layers, NPKM significantly increased POX activity, but decreased BG and CAT activities. Soil pH can regulate enzyme activities and synthesis in acidic soil in a tropical region with a significantly positive correlation with POX activity. Compared with NPK, the relatively lower Cp/SOC and higher carbon quality index (CQI) indicated higher SOC stability (Cp/SOC) in NPKM. The redundancy analysis results revealed that the dominant factors affecting SOC stability were NH4+-N, pH, POC and MBC in NPK, and available phosphorus, BG, and pH in NPKM. In the three fertilization treatments, the POX was the dominant factor affecting the CQI. Conclusively, half of the chemical N fertilizer plus half of the manure application could facilitate SOC stability by mediating soil C mineralization and enzyme activities in the rubber plantation of Hainan Island, China.