Simple Summary Alpine sandy areas in the Gonghe Basin, which had been subjected to four afforestation measures, exhibited a gradual increase in water content, nutrient content, enzymatic activities, and bacterial community richness and diversity with succession from the bare sand stage to an algae crust and then to a moss crust. In particular, the above indicators for the two types of biological soil crusts had higher values at the Populus simonii plantation (YY) site than at other afforested sites. Effective phosphorus and organic matter were the primary environmental factors affecting bacterial community structure in algae and moss crusts, respectively, and the activities of four types of enzymes were significantly correlated with the relative abundance of most major bacterial phyla. The functional prediction results showed that YY preserved the balance of primary functions while offering precise support for the physiological characteristics and ecological needs of different crust types in the secondary functions. A comprehensive analysis of the indicators revealed that YY was more favorable for the development of biological soil crusts.Abstract A good understanding of the effects of different afforestation measures in alpine sandy land on the physicochemical properties, enzymatic activities, and bacterial community structure of such crusts enables elucidation of the succession patterns of biological soil crusts and provides a theoretical basis for precise optimization of desertification control programs in alpine sandy land. In the present study, four afforestation measures-Salix cheilophila+ Populus simonii (WLYY00), S. cheilophila (WL), P. simonii (YY), and Caragana korshinskii (NT00) plantations-were adopted. The physicochemical properties and enzymatic activities of bare sand, algae crust, and moss crust in the four afforested sites were analyzed using Illumina high-throughput sequencing and PICRUSt2 functional prediction to investigate the bacterial community structure and function. Results indicated the following: (1) Water content, nutrient content, enzymatic activities, and bacterial community richness and diversity increased stepwise with succession from the bare sand stage to algae crust and to moss crust. The enhancement effect of YY on the above indicators and fine particle content was most prominent. (2) The primary environmental factors affecting bacterial community structure in algae and moss crusts were adequate phosphorus and organic matter, respectively, and the correlations between the activities of the four enzymes and the bacterial community structure are also quite close. (3) Functional prediction indicated that metabolism was the main primary function of biological soil crusts at the various sample sites. YY maintained the balance of primary functions and provided precise support for the physiological characteristics and ecological needs of different crust types in the secondary functions. In conclusion, among the four types of afforestation measures with a restoration period of 24 years, YY provided a greater advantage in improving the nutrient content, bacterial community structure, and functional potentials of biological soil crusts. The results of this study can serve as a scientific reference for screening of afforestation measures and protecting and utilizing biological soil crusts during the ecological restoration of alpine sandy lands in the present study area and other regions.