The ecological restoration of degraded alpine steppe is a critical component of ecological conservation efforts on the Qinghai–Tibetan Plateau. In this study, we investigated the effects of fertilization, reseeding, and combined fertilization with reseeding restoration measures on the vegetation community, soil properties and microbial community diversity in degraded alpine steppe through field vegetation surveys, and soil microbial high-throughput sequencing at an experimental site of fertilized and reseeded grassland restoration located in the Yellow River Source area. The results demonstrated the following: (1) both reseeding and combined fertilization with reseeding restoration measures significantly affected grassland vegetation community structure and diversity; (2) fertilization and combined fertilization with reseeding restoration measures significantly affected soil pH and total phosphorus (TP) content; (3) while fertilization and combined fertilization with reseeding restoration measures markedly altered microbial community structure, reseeding alone significantly affected microbial diversity. Co-occurrence network analysis revealed that soil microbial communities were significantly influenced by fertilization restoration measures; redundancy analysis (RDA) showed that microbial communities under fertilization and combined fertilization with reseeding restoration measures were primarily governed by soil TP, whereas those in control and reseeding plots were strongly associated with soil pH and organic carbon (SOC). This study explored effective restoration measures suitable for degenerating alpine steppe in the Yellow River Source area, aiming to provide a scientific basis and technical support for the ecological protection and restoration of the Three-River Headwaters.