Cover cropping has emerged as a pivotal sustainable agronomic practice aimed at enhancing soil health and sustaining crop productivity. To quantify its effects across diverse agroecosystems, we conducted a meta-analysis of 1877 paired observations from 114 studies (1980–2025) comparing cover cropping with bare fallow during fallow periods in major cereal systems across China. Cover cropping significantly reduced soil bulk density by 6.1% and increased key soil nutrients including total nitrogen (+13.1%), total phosphorus (+15.6%), hydrolysable nitrogen (+9.3%), available phosphorus (+11.1%), available potassium (+12.4%), soil organic matter (+11.7%), and microbial biomass carbon (+41.1%). Leguminous cover crops outperformed non-legumes in enhancing nitrogen availability, reflecting biological nitrogen fixation. Mixed-species cover crop mixtures showed superior benefits over monocultures, likely due to complementary effects on nutrient cycling and soil structure. Soil texture and initial soil organic carbon significantly moderated these outcomes. Furthermore, although overall soil pH remained stable, cover cropping exhibited a clear buffering effect, tending to regulate soil pH toward neutrality. Meta-regression analyses revealed a diminishing positive effect on total nitrogen (TN), available potassium (AK), and microbial biomass carbon (MBC) with an extended duration of cover cropping, suggesting potential saturation effects. These results underscore the context-dependent efficacy of cover cropping as a strategy for soil quality enhancement. Optimizing cover crop implementation should integrate the consideration of inherent soil characteristics, baseline fertility, and species composition to maximize agroecosystem resilience and sustainability.