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Saline-alkali land is the main reserve soil resource. The amount of arable farmland soil can be increased through improvement and utilization of saline-alkali land. Bio-organic fertilizer is an effective saline-alkali soil conditioner, but there are few studies on the improvement of saline-alkali soil with traditional Chinese medicine residues (TCMRs). In this study, an organic fertilizer made from Ganoderma lucidum residue (GLR) was mixed with saline-alkali soil at different proportions; physicochemical properties, enzyme activity, and microbial community characteristics of the soil were investigated. The results showed that the soil pH, as well as bulk density and electrical conductivity were significantly reduced, while the soil moisture content and porosity were significantly increased after the GLR organic fertilizer incorporation. Soil invertase and soil amylase activities significantly increased, as well as the diversity and richness of the soil microbial community structure. The abundance of the dominant phyla, Bacteroidota, Actinobacteriota, Chloroflexi, Firmicutes, and Basidiomycota, increased, while the abundance of the dominant Proteobacteria and Ascomycota phyla decreased. The best improvement effect is obtained when the application ratio of GLR organic fertilizer is 25%. The findings showed that TCMRs have positive application prospects in saline-alkali soil improvement.