In order to investigate the changes of soil enzyme activity and bacterial community structure after fertilizer application and to provide basic data to support the promotion of food waste compost on farm, flue-cured tobacco growing soils in central Yunnan were taken as study object, different application rates of food waste compost (base fertilizer) were designed: no fertilizer control (CK), low fertilizer application rate (8 t/hm², FWL), medium fertilizer application rate (16 t/hm², FWM), and high fertilizer application rate (24 t/hm², FWH). The results show that compared with CK, FWH significantly increases soil pH, the contents of organic carbon, total nitrogen, total phosphorus, alkaline soluble nitrogen and effective phosphorus, the activities of urease, acid phosphatase, fluorescein diacetate hydrolase activity (↑0.39%-89.42%), soil bacterial OUT number (↑12.91%), Chao index (↑11.20%), Ace index (↑11.37%). The relative abundance of Proteobacteria is increased with increasing fertilizer application, while Acidobacteria is decreased. Both membrane transport and carbohydrate metabolism of the bacterial community are significantly enhanced after fertilization. Urease and acid phosphatase activities, pH, total nitrogen, total phosphorus, alkaline nitrogen and effective phosphorus all have effects on the community composition and diversity of soil bacteria, with alkaline nitrogen and urease activity being the most important factors regulating the bacterial community.