Fertilization is an important agricultural practice for increasing crop yields and influencing soil properties. A field experiment was conducted in the period of 2006-2011 in southeastern China, to investigate the effects of fertilization regimes on tea (Camellia sinensis [L.] Kuntze) yields, soil chemical properties, and soil bacterial and fungal communities. The field experiment included six treatments: (1) unfertilized control (CON); (2) chemical fertilizers (NPK); (3) half-chemical fertilizers plus half-organic manure (1/2NPKOM); (4) organic manure fertilizers (OM); (5) half-chemical fertilizers plus half-organic manure plus legume stover returned (1/2NPKOM+L), and (6) chemical fertilizers plus legume stover returned (NPKL). Results showed that, compared to the control, NPK treatment showed no significant effect on soil organic matter (SOM), total N (TN), total P (TP), total K (TK), available N (AN), available K (AK) and tea yields, but showed the lowest bacterial Shannon index of 1.714 and the lowest value of 2.002 for fungal Shannon index. Organic manure treatment had the richest diversity of soil bacterial community with Shannon index of 2.542, and the highest levels of soil essential nutrients, including SOM (30.03%), TN (2.90 g kg-1), TP (1.35 g kg-1), AN (245.30 mg kg-1), AP (57.00 mg kg-1), and AK (271.80 mg kg-1), followed by 1/2NPKOM+L, which appeared the maximal tea yields of 6772 kg ha-1. Organic manure amendment was a key factor in determining soil properties and productivity. Base on soil quality and tea yields, both OM and 1/2NPKOM+L treatments were recommended as better choices of fertilization practices for tea soils in southeastern China. These findings provided a better understanding of the importance of fertilizations in promoting soil fertility, crop yields, and altering soil microbial diversity, leading to selection of scientific fertilization practices for sustainable development of agroecosystems.