Desertification poses a severe challenge in China. Although long-term sand control measures have proven effective, the extensive and challenging nature of sandy land necessitates systematic research to identify optimal sand control measures for soil amelioration, thereby promoting ecological restoration in sandy areas. This study focused on the Gonghe Basin to assess the effectiveness of four 24-year afforestation treatments-Salix cheilophila + Populus simonii, S. cheilophila, P. simonii (YY), and Caragana korshinskii-compared to untreated mobile dunes. Surface soils (0-10 cm and 10-20 cm) were analyzed for physicochemical properties, enzyme activities, and bacterial community structure using Illumina high-throughput sequencing and PICRUSt2 functional prediction. All afforestation treatments significantly improved soil quality, increasing fine particle content, moisture, nutrients, enzyme activity, and microbial richness and diversity, especially in the topsoil. Bulk density and pH were notably reduced. Among the treatments, YY demonstrated the most substantial improvements. pH emerged as the primary factor influencing bacterial community structure, with enzyme activities also playing a significant role. Metabolism was the dominant functional category across all sites, while YY enhanced environmental information processing functions in the topsoil. Secondary functions showed high redundancy across treatments. These findings confirm that afforestation can effectively rehabilitate degraded alpine sandy soils, with the YY treatment offering the greatest benefits. The study provides a scientific basis for optimizing sand control measures and supports broader ecological restoration efforts in similar environments worldwide.