<p>The present study examined the effects of a watermelon–Chinese chive rotation on watermelon fusarium wilt. A greenhouse plot was continuously planted with watermelon for five years. The soil treatments comprised a watermelon–Chinese chive rotation (T) or no rotation (CK). The incidence and disease index of watermelon fusarium wilt were monitored at the fruiting early stage, the fruit swelling stage, and fruit maturity stage. The soil bacterial communities were analyzed at different growth stages by high-throughput sequencing, and bacterial functions were predicted by PICRUSt. The incidence of watermelon fusarium wilt was reduced by the rotation, and the onset of wilt was delayed. The average control efficacy was 95.2%. The watermelon–Chinese chive rotation significantly increased the Chao1 index, ACE index, and specificity of the soil bacterial community. Principal component analysis showed that the rotation altered the structure of the soil bacterial community at the phylum and genus levels. The composition of the soil bacterial community differed among cropping practices and stages. The rotation increased the relative abundance of Proteobacteria and Acidiobacteria at each stage. The relative abundances of the two phyla were significantly different between the growth stages and treatments. The rotation resulted in increases of Pseudomonas and Nitrospira and decreases of AKYG587 and Flavobacterium. Several genera were significantly different among stages in the continuous and rotation cropping. The PICRUSt gene prediction analysis showed that metabolism comprised the largest proportion (72.3%–74.8%), and there were differences in the secondary functions of metabolism.</p>