Chemical fertilizer is widely used in agricultural fertilization, but over-fertilization has caused soil quality degradation. Some studies have shown that the application of organic fertilizer is beneficial to soil quality, but there are few studies researching the long-term organic fertilizer application effect on tea plantation soil. In this paper, we studied the physical and chemical properties and microbial communities of tea plantation soil through long-term field experiments by applying organic fertilizer with equal nitrogen amounts. The experiment showed that the soil’s physical and chemical properties were improved after long-term application of total organic fertilizer. Respectively, the soil organic matter (SOM), available potassium (K), available zinc (Zn), available copper (Cu), and pH were significantly enhanced, the soil bulk density was significantly increased, the water-stable aggregates were improved, the soil microbial diversity was increased. It was found that the main bacteria in tea soil were Proteobacteria, Acidobacteria, and Actinobacteria. Moreover, results from redundancy analysis showed t hat t he S OM ( p = 0 .001), A lkali h ydrolyzed n itrogen ( p = 0 .049) a nd p H ( p = 0 .008) h ad significant effects on the soil bacterial community composition. Thus SOM increased the relative richness of non-dominant bacteria, such as Bacteroidetes, Gemmatimonadestes, and Firmicutes. Overall, our results suggest that the use of organic fertilizer instead of chemical fertilizer could effectively improve the quality of tea plantation soil.