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The application of beneficial microbial consortium can effectively improve plant disease resistance and its growth. Various fungi were compounded with <i>Bacillus velezensis</i> LJ02 and applied to watermelon plants in this paper. The results showed that the microbial consortium T2 (compounded <i>Bacillus velezensis</i> LJ02 with <i>Aspergillus aculeatus</i> 9) can effectively control gummy stem blight and powdery mildew in watermelon, while the control effect reached 83.56% and 70.93%, respectively (<i>p</i> < 0.05). Compound treatment improved the diversity and richness of the rhizosphere microbial community structure, and the relative abundance of <i>Caulobacterales</i> and <i>Xanthomonadaceae</i> significantly increased after applying T2 to the soil. Meanwhile, the internode length was significantly decreased 28% (<i>p</i> < 0.05), and the maximum leaf length increased 10.33% (<i>p</i> < 0.05). In addition, the microbial consortium delays the maturity of watermelon vegetables. By studying the effects of microbial consortium on watermelon seedlings, our study provides a theoretical basis for the popularization and application of the compound inoculant.