Abstract: Biochar-immobilized microorganisms offer an effective strategy to overcome the limitations of free microorganisms—such as poor viability, colonization difficulty, and low efficiency—in complex environments. It provides a novel approach to address key challenges in tobacco production, including soil-borne diseases, continuous cropping obstacles, and quality and safety. This review summarizes the physicochemical advantages of biochar as a microbial carrier and elucidates the synergistic mechanisms between biochar and microorganisms, encompassing physical protection, chemical buffering, electron transfer, and microbial community regulation. This review highlights the application progress of biochar-loaded microorganisms in green control of tobacco soil-borne diseases, soil remediation, rhizosphere health cultivation, and sustainable tobacco production, demonstrating its potential to reduce pesticide and fertilizer inputs while ensuring raw material safety. Finally, current challenges and future directions are discussed, including the development of tobacco-specific functional biochar-microbe complexes, construction of synthetic rhizosphere microbial communities, and integrated strategies for soil remediation, carbon sequestration and fertility improvement, and quality and efficiency enhancement.