Green manuring can synergistically benefit agricultural production and environmental sustainability, and the understanding of microorganisms in promoting carbon sequestration and crop productivity is still to be strengthened. This study aimed to explore how microbiomes under green manuring affect peanut yield and soil organic carbon (SOC) dynamics. A six-year field experiment was conducted to compare two cropping regimes, peanut continuous monoculture (P) and peanut-Orychophragmus violaceus rotation (PO). The multi-year peanut yields were monitored. In 2022, SOC dynamics (C contents, mineralization rate, and enzyme activities) and microbial characteristics (diversity, community composition and occurrence network) were examined in the rhizosphere, bulk soil, and bulk soil aggregates. PO alleviated the continuous monoculture obstacles by elevating soil pH, increasing NO3--N level, and enhancing enzyme activities. Moreover, PO promoted bacterial alpha diversity and network complexity, decreased fungal richness and network complexity, selectively enriched beneficial microbes such as Bacillus and Aspergillus, and inhibited pathogenic fungi like Fusarium and Coniochaeta, resulting in an average yield increase of 41.0%. Nevertheless, the addition of excessive nitrogen and intensified carbon limitation by PO constrained the r-strategist carbon decomposers, as indicated by the reduction in bulk soil Kc (by 23.9%), and stimulated the K-strategist carbon decomposers, as shown by the decrease of SOC. Although PO increased peanut yield and improved soil health, it is unfavorable for SOC sequestration in the long run, thus should be applied with caution in the leguminous field. This study highlighted the synergism of high crop productivity and promoted carbon sequestration to develop sustainable and green agriculture.