Abstract: Complex and dynamic interactions among soil microorganisms are ubiquitous, playing pivotal roles in sustaining ecosystem functions and safeguarding plant health. Trichoderma spp. and Bacillus spp. represent the most extensively utilized beneficial microorganisms in agroecosystems, demonstrating remarkable potential in biocontrol, growth promotion, yield enhancement, and stress resilience. As research focus shifts from single-strain functional analysis to multispecies synergistic mechanisms, the interactions between Trichoderma and Bacillus have garnered increasing attention. Although these taxa exhibit antagonism on laboratory media, current evidence indicates that their relationship in natural environments transcends simple antagonism or competition. Bacillus can stably colonize Trichoderma hyphae through biofilm-mediated mechanisms involving genes such as eps and tasA, establishing a hyphal–bacterial interfacial microzone with distinct physicochemical properties. During this association, Trichoderma tolerates antifungal lipopeptides secreted by Bacillus via specific transporters (e.g., TgMFS4), repurposing these compounds into environmental cues that trigger its own stress responses—such as T22azaphilone biosynthesis and chlamydospore formation—thereby shifting the interaction from antagonism to coexistence. This transition is dynamically regulated by abiotic factors including inoculation sequence, pH, nitrogen source, and temperature. Concurrently, the mycelial network formed by Trichoderma provides physical support and dispersal channels for Bacillus, enabling it to overcome soil heterogeneity and achieve stable rhizosphere colonization. Greenhouse and field trials have substantiated that co-application of Trichoderma and Bacillus significantly enhances crop disease resistance and productivity. This synergistic effect, superior to that of single-strain inoculation, is achieved through multilayered biocontrol barriers, induction of plant systemic resistance (ISR), and coordinated promotion of nutrient uptake. However, critical knowledge gaps remain regarding the molecular basis of specific ligand recognition on hyphal surfaces by Bacillus, the regulatory interplay between quorum sensing and fungal metabolism, and the intricate networking within the plant–Trichoderma–Bacillus–pathogen continuum. Future research should leverage multi-omics technologies to elucidate the dynamics of bacterial transcriptional reprogramming and fungal metabolic responses during hyphal colonization. Additionally, employing synthetic biology to engineer strains with enhanced synergy, developing advanced formulations such as microencapsulation and slow-release systems, and establishing precision application protocols based on indigenous microbiome profiles will be essential to translate the mechanistic understanding of Trichoderma–Bacillus consortia into large-scale agricultural applications.