Aims: Cotton continuous cropping might cause the soil-borne disease Verticillium wilt in agricultural production. Crop rotation has been shown to be an effective method for controlling this disease. The objectives of this study were to evaluate the effects of cotton-maize rotation (CMR) and cotton-maize-broccoli residues rotation (CMBR) on incidence of cotton Verticillium wilt (CVW), soil microbial community structure and function.Methods: qPCR was used to determine the populations of V. dahliae. Soil microbial community structure and function was analysed using metagenomics analysis.Results: Results demonstrated that the disease incidence significantly decreased by 87.19% and 98.93%, and the populations of V. dahliae decreased by 67.07% and 84.36% under the CMR and CMBR treatments, respectively. There were significantly differences in bacterial communities under the CMR and CMBR treatments. Redundancy analysis revealed that the structures of microbial communities were mainly driven by available potassium (AK) and pH. Spearman’s correlation analysis showed that most of KEGG pathways in bacterial community were negatively with pH, positively with NH4+-N and AK. The abundances of NifH, AmoA, NirK, and NarG genes (involved in nitrogen cycling), PfkABC, FbaB, PGAM and KdpgA genes (carbon cycling), and Sir, Sat, and CysND (sulfur cycling) were enriched by the CMR and CMBR treatments.Conclusions: CMR and CMBR could change the bacterial community structure and nutrients cycling in cotton rhizosphere, decrease the populations of V. dahliae in soil, therefore significantly reduce the incidence of CVW.