The aim of this study was to investigate effects of long-term fertilization on lateritic red soil fertility in cropping-green manure planting system and provided corresponding sustainable management. A long-term field experiment was conducted to study the effects of different fertilization method on soil nutrients, enzyme activities and microbial traits in lateritic red soil. The results showed that : Compared to the control treatment, long-term fertilization significantly increased the soil organic matter, alkali solution nitrogen, phosphorus, rapidly-available potassium nutrient, and improved the soil sucrose invertase, urease and phosphatase activities, and increased the content of soil microbial biomass carbon and nitrogen and microbial community species richness, dominance, evenness. The long-term fertilization increased soil nutrient content by 4.5%～117.2%, enzyme activity by 4.9%～68.1% and microbial diversity by 3.2%～71.9%, respectively. The microbial biomass carbon and nitrogen content were increased by 7.8%~36.9% and 21.4%~65.7%, and the most significant effect was observed as following: Organic manure (M), organic and inorganic fertilizer treatment (NPKM) and straw with inorganic fertilizer treatment (NPKS). The significant correlations were found between soil nutrient, soil enzyme activity, microbial diversity as well as microbial biomass carbon and nitrogen (p＜0.05). In summary, the long-term single organic fertilizer or organic combined with inorganic fertilization was a good measure for fertility improvement in soil of cropping-green manure planting system.