Aims <p>Deterioration of anthropogenic-alluvial soil is becoming a serious concern. This study aims to explore the effect of green manure cultivation and derived microbial consortium on amelioration of deteriorated anthropogenic-alluvial soil and crop growth.</p> Methods <p>Field experiments, microbiome analysis and physiochemical analysis were performed to explore the key microbial consortium and its positive effect.</p> Results <p>Both <i>Vicia villosa</i> cultivation during the period of wheat turning yellow (Vvi) and its cultivation after <i>Triticum aestivum</i> harvest (TaeVvi) drastically reduced the salinity and pH values, and increased the levels of organic matters, total nitrogen, available nitrogen, and available phosphorus in the anthropogenic-alluvial soil. As revealed by microbiome analysis and culturomics, the consortium of <i>Acinetobacter</i> and <i>Bacillus</i> was enriched by the green manure cultivation, and contributed to the decreased salinity and pH, and the increased organic matters, total nitrogen, available nitrogen, and available phosphorus in deteriorated anthropogenic-alluvial soil. Moreover, the consortium accelerated nutrient accumulation and chlorophyll synthesis in the leaves of the <i>Brassica rapa var. glabra</i> plants, leading to the increase in crop yield.</p> Conclusions <p><i>V. villosa</i> cultivation and the derived <i>Acinetobacter</i> and <i>Bacillus</i> consortium remarkably improved anthropogenic-alluvial soil quality and crop production. This study sheds a light on green manure-reshaped microbial consortia for further application in soil amelioration and crop production.</p>