Different fertilization measures affect the soil’s physical and chemical properties and bacterial community structure, which in turn affects the growth environment and yield of maize seed production. Therefore, rational fertilization measures are important in maintaining and improving soil fertility and promoting maize crop growth. Research on fertilization practices in maize fields for seed production can help to increase agricultural productivity while protecting and enhancing soil health and achieving sustainable agricultural development. To clarify the effects of different fertilization measures on soil bacterial communities in seed corn fields, 16S rRNA high-throughput sequencing technology and PICRUSt method were used to explore the soil under different fertilization measures (CK as control, effects of single application of liquid organic fertilizer (M), single application of bacterial agents (BF), and combined application of liquid organic fertilizer and bacterial agents (M + BF)) on soil bacterial community structure characteristics and ecological functions. Proteobacteria (20.14–25.30%), Actinobacteriota (18.21–20.47%), Actinobacteriota (13.55–22.00%), and Chloroflexi (14.24–17.59%) were the dominant phyla. Bacillus, RB41, Arthrobacter, and Sphingomonas were the dominant genera. M + BF treatment significantly increased the relative abundance of Planctomycetota. The relative abundance of Bacillus and PaeniBacillus in M treatment decreased considerably, while the relative abundance of Turicibacter increased significantly. The relative abundance of Sphingomonas was reduced considerably in M and M + BF treatments. The relative abundance of Subgroup 10 decreased significantly after BF and M + BF treatments. BF treatment significantly increased the relative abundance of Skermanella. Redundancy analysis showed that alkali-hydrolyzed nitrogen (p = 0.044) was the main environmental factor affecting soil bacterial communities under different fertilizer treatments. PICRUSt function prediction results showed that metabolism was the main functional component of bacteria, accounting for 78.45–78.94%. The abundance of functional genes for terpenoid and polyketone metabolism, the endocrine system, the excretory system, and the immune system of the soil bacterial community was significantly increased under M treatment, while the abundance of functional genes for the digestive system was decreased considerably. Different fertilizer cultivation measures changed soil bacterial community composition and ecological function in maize fields. These results can provide a theoretical reference for the study of bacterial community succession characteristics in maize fields and the determination of appropriate fertilizer cultivation measures.