Rapeseed cake is an important agricultural waste and it has the potential to improve soil fertility, crop productivity and microbial activities. Nonetheless, the effects of rapeseed cake on microbes of tobacco rhizosphere have not studied yet. Therefore, this study was conducted to investigate the effects of rapeseed cake fertilizer on the inter-root soil microbial community of roasted tobacco. The present study was comprised of different proportions of nitrogen replacement fertilizers such as rapeseed cake fertilizer (N30:30%, N60:60%, N100:100%), and recommended nitrogen application as control. The results of diversity analysis showed that cake fertilizer significantly increased the Ace and Chao indices of soil microbial populations, and Shannon and Invsimpson indices were significantly higher. Furthermore, cake fertilizer also significantly increased the relative abundance of Actinobacteria, Ascomycetes, Intrasporangium, Chaetomium and Mortierella and decreased the relative abundance of Firmicutes, Basidiomycota and Fusicolla. Moreover, cake fertilizer also significantly increased the abundance of stress-tolerant bacteria and animal pathogen-dung saprotroph-endophyte-epiphyte-plant saprotroph-wood saprotroph fungi, and decreased the abundance of their potentially pathogenic and anaerobic bacteria and unknown saprophytic types and plant pathogenic fungi. Further, available phosphorus (AP), soil organic carbon (SOC), microbial biomass carbon (MBC) and microbial biomass nitrogen (MBN) were identified as the main factors affecting the structure of the inter-root soil microbial community of baked tobacco. In conclusion, rapeseed -cake based fertility could be an important strategy to modulate the composition of bacterial and fungal communities in tobacco rhizosphere by improving soil properties, and decreasing the abundance of pathogenic bacteria.