Fusarium root rot (caused by Fusarium verticillioides) is a destructive soilborne disease in maize, significantly reducing crop yields. The root symbiotic fungi Trichoderma species have been confirmed as effective biocontrol microbes for Fusarium root rot; however, the mechanistic role of Trichoderma-induced endophytes in suppressing Fusarium root rot in maize remains unclear. This study found that Trichoderma harzianum T30 significantly reduced the abundance of pathogens by 48.9% and increased the abundance of potentially antagonistic Bacillus strains (33%) in the root endophytic bacterial community. In addition, the hyd1 gene in T. harzianum T30 induced a 7.5-fold upregulation of ZmOPR7 in maize roots compared to the Δhyd1 mutant treatment, a gene related to the jasmonic acid (JA) pathway. Further, several endophytic Bacillus strains were specifically induced by a hyd1-overexpressing strain, including B. amyloliquefaciens MX66, B. velezensis C9, and B. velezensis GAGAN3. Three endophytes significantly (p < 0.05) reduced Fusarium root rot incidence in maize by 46.6–55.0% and upregulated the expression of jasmonic acid/ethylene (JA/ET) pathway-related genes (ZmOPR7, ZmOPR8 and ZmEIL1) by 5.4-, 1.5-, and 4.6-fold, respectively, compared to untreated controls. Meanwhile, the Bacillus strain also improved maize plant growth. This study examined how overexpression of the T. harzianum elicitor gene hyd1 (in the OE-hyd1 strain) affects the colonization dynamics of beneficial endophytic bacteria in maize roots. Additionally, it further suggested the contribution of selected endophytic Bacillus strains in suppressing Fusarium root rot in maize.