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The large outbreak of banana Fusarium wilt has become a bottleneck limiting the industry’s development, and crop rotation is a cost-effective and essential measure to overcome the obstacles of banana crop monoculture. The present work was carried out to explore the mechanisms of how changes in soil chemical properties and the reestablishment of soil microorganisms in high-incidence soils are affected by crop rotation and plant residue. In this study, pineapple–banana crop rotation and pineapple residue amendment were carried out to alleviate banana Fusarium wilt, and their effects on bacterial and fungal communities were analyzed using the MiSeq Illumina sequencing platform. Both pineapple–banana rotation and residue addition significantly reduced disease incidence. Moreover, pineapple rotation and residue amendment altered the bacterial and fungal community composition. The taxonomic and phylogenetic alpha diversity of bacteria and fungi significantly increased against disease suppression and nutrition competition. The relative abundances of the Burkholderia, Pseudomonas, Elaphocordyceps, Penicillium, and Talaromyces genera were higher, and the number of Fusarium was significantly lower in rotational soil than in banana monoculture soil. Finally, linear models (LM) showed that the Burkholderia and Talaromyces in crop rotation, and Aspergillus in residue amendment had a significantly negative relationship to disease incidence, which plays a key role in Fusarium reduction. To consider the economic benefits and protect the vitality of the soil, this study suggested that pineapple–banana rotation and pineapple residue amendment both could be considered for the sustainable management of banana wilt.