In this study, 16S rRNA gene high-throughput sequencing was used to compare and analyze the differences in soil bacterial community structure and composition under 4 multiple cropping modes including flue-cured tobacco-soybean(D), flue-cured tobacco-maize(Y), flue-cured tobacco-rice(S) and flue-cured tobacco-autumn fallow(L)，as well as the relationship between different multiple cropping modes and the incidence of tobacco black shank. The results showed that the incidence of tobacco black shank in modes D,Y and S were 59.35%, 39.81% and 27.71%, respectively, which were significantly lower than that in mode L, which was 80.22%. The diversity of soil bacterial communities in modes L, D, Y and S increased gradually. The sequencing results showed that Proteobacteria, Chloroflexi and Acidobacteria were the dominant phyla in soil bacterial community of tobacco field, while Chujaibacter, Rhodanobacte, uncultured_Acidobacteria_bacterium and Acidibacter were the common dominant genera, and the abundance of dominant phyla and common dominant genera were different among different multiple cropping modes. Compared with the L mode, the relative abundance of Chujaibacter, Rhodanobacter and Acidothermus in other 3 modes decreased significantly while the relative abundance of Candidatus_Solibacte, Anaerolinea and Haliangium were increased. The abundance of Chujaibacte, Rhodanobacter, Acidothermus and Occallatibacte were significantly positively correlated with the incidence of black shank disease, while the abundance of Candidatus_Solibacter, Anaerolinea and Haliangium were significantly negatively correlated with the incidence of black shank disease. Compared with the flue-cured tobacco-autumn fallow continuous cropping mode, the other 3 multiple cropping rotation modes could alter the bacterial community structure which was conducive to disease resistance, thereby reducing the occurrence of black shank disease in flue-cured tobacco.