In this study, different crop rotations were used to evaluate their ecological effects on cucumber fusarium wilt, root-knot nematode incidences, and host fungal microbiome structure in the plastic shed of North China. We used the high-throughput Illumina HiSeq technique to study the fungal rhizomicrobiome and further characterize the fungal community composition into beneficial and pathogenic microbial genera. The finding of this study suggested that rotation with cover crops altered the fungal microbiome structure by which beneficial fungal characters induce and pathogenic microbes decreases. Such rotational-assisted microbial manipulation caused a significant impact on the control of fusarium wilt, root-knot nematode incidences, and promoted cucumber growth and fruit quality.