Green manure-tobacco rotation system has proven to be an effective strategy for improving soil nutrients and alleviating soil-borne fungal diseases. However, the differential efficacy of various green manures against tobacco root rot and their underlying microbial regulatory mechanisms remains unclear. Through pot-based experiments, this study systematically evaluates the disease-suppressive effects of two green manure, smooth vetch ( Vicia villosa) and rape ( Brassica campestris), applied at two incorporation rates on tobacco root rot (caused by Fusarium solani). Results indicated that green manure incorporation significantly reduced pathogen abundance by 36.1-64.7%, decreased root rot disease incidence by 10-20%, with smooth vetch exhibiting superior disease suppression compared to rape. Smooth vetch incorporation enriched a higher abundance of Bacillus spp. (Bacillus niacini and Bacillus megaterium) in rhizosphere soil, increasing by more than 2 times compared to no incorporation . Co-occurrence network analysis identified four microbial modules, among which Module 0 exhibited a significant negative correlation with pathogen related abundance. Within Module 0, bacterial taxa, particularly Bacillus spp., occupied central positions with extensive node interactions, while fungi maintained higher relative abundance. This module also contained other disease-resistant communities, including Paenibacillus, Lysobacter soli, Chaetomium sphaerale and Rhizopus arrhizus. Notably, smooth vetch treatment enhanced soil available nutrients, (especially alkaline nitrogen content) more effectively than rape treatment, favoring the increase of these disease-resistant communities. Collectively, smooth vetch demonstrates superior capacity in enhancing resistance to tobacco root rot and reducing disease incidence, offering an effective solution for tobacco soil-borne disease prevention and control.