Saline-alkali soils of northern China are prone to waterlogging after degradation caused by overuse. The effects of biochar (40 t/ha) were tested relative to the physico-chemical properties of maize rhizosphere soil, the composition and function of the soil bacterial community, and its response to sudden waterlogging. Biochar treatment decreased the pH and bulk density of the soil and increased soil organic carbon (SOC), available nitrogen (AN), and available phosphorus (AP). The relative abundance of bacteria (Proteobacteria, Actinobacteria, Bacteroidetes, and Nitrospirae) also increased, along with the activities of soil enzymes, such as dehydrogenase, β-glucosidase, and alkaline phosphomonoester. The response of soil microbial enzymes to biochar addition was induced by changes in the soil physical properties (pH, soil moisture content, and soil respiration (BR)). Changes in the bacterial community structure were driven by soil nutrients and physical characteristics (AN, AP, SOC, pH, moisture, water-stable aggregate stability rate, BR, and bulk density). After waterlogging, soil with biochar demonstrated high water permeability and improved soil respiration. The relative abundance of soil bacteria and enzyme activities remained higher in the biochar plot than in the no-biochar plot. Biochar maintained the growth and vitality of maize roots in unfavorable environmental conditions, thus ensuring high yields.