In this study, the control effects on soil-borne diseases in cantaloupe and the dynamic change of eukaryotic microbial community during the whole growth period were investigated by using the Brassica campes and Brassica juncea seed meals as soil green fumigants. The results showed that the two kinds of seed meals could effectively control soil-borne diseases, showing a similar control efficacy but significant differences in the disturbance of soil microbial communities and the enrichment of rhizosphere microorganisms to that of dazomet. Both Brassica campes and Brassica juncea seed meals not only significantly reduced the richness and diversity of eukaryotic microorganisms but also selectively promoted the recovery and enrichment of specific microorganisms in the soil, thus, colonized the beneficial microorganisms in the rhizosphere. During the process, phylum Ascomycota dominated the change of the microbial community composition and played an important role in the construction of beneficial microbial communities in the rhizosphere. Moreover, the abundance of species Aspergillus lentulus and unknown species (OTU_213) showed a significant negative correlation with incidence rate, indicating they inhibited the colonization of pathogenic fungi in the rhizosphere. On the contrary, dazomet had less effect on the colonization of rhizospheric beneficial microorganisms and the composition of soil microbial community than seed meals.