Overuse of chemical fertilizers to maintain tea production has caused many adverse effects in tea plantations and largely hampers the sustainable development of the tea industry. Applying bio-organic fertilizer (BOF) to achieve the goal of sustainable agriculture has become popular because of its advantages, such as its pollution-free nature, considerable amount of beneficial microbes and soil-friendly organic materials. However, the effects of BOF application on tea plantation soil remain an open question. Herein, we carried out a 3-year pot experiment with four treatments, including control without fertilization (CK), 100% chemical fertilizer (CF), 50% chemical fertilizer +50% BOF (CFOF) and 100% BOF (OF), to explore the effects of BOF application on soil fertility and bacterial community in tea plantations. The results showed that BOF application could increase soil fertility in both bulk and rhizosphere soils and improve the biomass of tea leaves. In addition, the nutrient level change caused by BOF application significantly changed bacterial community diversity and composition and accounted for 74.91% of the community variation. CFOF and OF treatments significantly increased the bacterial Chao1 and Shannon indices compared to CF treatment (p < 0.05). Moreover, bacterial community composition was dominated by Betaproteobacteria (46.88%), Acidobacteria (11.29%), Alphaproteobacteria (9.69%) and Gammaproteobacteria (9.59%). BOF application increased the relative abundance of Alphaproteobacteria, Acidobacteria, Deltaproteobacteria and planctomycetes and decreased the relative abundance of Betaproteobacteria (p < 0.05). Furthermore, bacterial function prediction revealed that BOF application improved the N and C cycling processes and enhanced the co-occurrence network complexity in the bulk soils. Bacterial community functions and co-occurrence networks in the rhizosphere did not show similar results, indicating that rhizosphere bacterial communities were more affected by the rhizosphere effect than BOF application. All these findings verified our hypothesis that applying BOF in tea plantations could increase the biomass of tea plants by improving soil fertility and influencing the soil bacterial function groups. In summary, we suggested that BOF application could be a promising way to achieve the sustainable development of the tea industry.