This study investigated whether legume cover crops, particularly Vicia sativa L., improve soil fertility and fruit quality via microbial community remodeling, and whether this practice outperforms natural grass management in pear orchards. Five treatments were established: clean tillage (CK), natural grass (T1), Vicia sativa L. (T2), Vicia villosa Roth (T3), and a mixture of V. sativa and V. villosa (T4). High-throughput sequencing, soil biochemical assays, microbial co-occurrence network analysis, and PLS-PM were integrated to explore underlying mechanisms. Results showed that V. sativa significantly altered bacterial and fungal communities versus CK and T1, enriching beneficial taxa (Bradyrhizobium, Nitrospira, Mortierella, Tausonia) while suppressing pathogens (Alternaria, Fusarium, Curvularia). The V. sativa treatment also enhanced soil enzyme activities and nutrient availability, leading to increased fruit weight, soluble sugars, and ascorbic acid. PLS-PM revealed that legume treatments increased bacterial but decreased fungal abundance; bacterial communities positively correlated with soil nutrients and enzymes, whereas fungal communities showed negative correlations. Soil nutrients emerged as the primary factors associated with fruit quality improvement, with bacterial and fungal contrasting effects suggesting a potential microbial pathway. Collectively, V. sativa green manure optimized microbial structure by enriching beneficial microbes and suppressing pathogens, thereby improving soil health and pear fruit quality synergistically.