Currently, facility cultivation produces almost a third of all vegetables in China. The intensive production style has led to serious soil problems that need to be tackled. In this paper, a pot experiment was set up to evaluate the effects of optimized fertilization on vegetable growth and soil properties. Specifically, calcium, magnesium, boron and molybdenum were added on the basis of soil testing. The results showed that the growth of Chinese cabbage was significantly increased by optimized fertilization. The soil pH increased (by 3.82%), and EC decreased (by 8.54%). The abundance of culturable bacteria increased by 33.86%, whereas that of fungi decreased by 70.7%. The optimized fertilization increased the richness but not the evenness of soil microorganisms, increased the relative abundance of Proteobacteria, Firmicutes, Bacillus and Bacteroidetes, and decreased the relative abundance of Actinobacteria, Chloroflexi, and superphyla. Optimized fertilization inhibited the growth of Chytridiomycota and Mortierellomycota, especially the plant pathogen Fusarium. Moreover, balanced fertilization was beneficial in promoting various metabolic processes of soil bacteria. Soil water-soluble Ca, Mg, and available Mo might be the main factors driving the change in microbial groups.