Garden waste compost (GWC) has been applied as an amendment to improve the desalination efficiency, nutrient availability and diversity of the microbial community in coastal saline soil. Understanding the response of the microbial community to garden waste compost application is of great significance in coastal ecological restoration. Four treatments were established: CK, nonamended control; T1, application of 68 kg·m−3 garden waste compost; T2, application of 15 kg·m−3 bentonite; and T3, a mixture of garden waste compost and bentonite. In addition, soil physicochemical properties, soil enzymes, microbial biomass carbon and the soil microbial community were measured. The results show that T3 had a more significant effect on increasing soil enzymes, as well as microbial biomass carbon and nitrogen, urease, sucrase and dehydrogenase activities. Based on the relative abundance, microbial diversity and linear discriminant effect size (LEfSe) analyses, the amendments can be seen to have increased the microbial abundance and alpha diversity of the bacterial structure and also altered the microbial community structure. RDA and Pearson correlation analysis at the phylum level indicated that available nitrogen, total porosity, hydraulic conductivity, bulk density and EC were the primary determinants of microbial communities associated with this amendment. In conclusion, the application of garden waste compost enables more microorganisms to participate in the soil material cycle, indicating that garden waste composting is beneficial to the restoration of coastal soils.