Abstract: Microbial magnetic effect (MME) is an environmentally compatible intensification strategy that employs magnetic fields to modulate microbial growth and metabolism while restructuring community architecture. This approach facilitates the activation of pivotal enzymatic functions, enhances the efficiency of both intracellular and extracellular electron transfer, and selectively enriches functional microbial consortia, thereby markedly elevating the overall catalytic activity and metabolic efficacy of microbial systems. This review elaborates on the influence of MME on microbial activity, growth metabolism, and community structure, and systematically summarizes recent advances in the applications of this technology, such as anaerobic digestion of organic waste for methane production, dark fermentation for hydrogen production, and synthesis of high-value chemicals. Results show that in anaerobic digestion for methane production, magnetic fields significantly increase methane yield and system stability by enhancing substrate conversion, electron transfer, and microbial community synergy. In dark fermentation for hydrogen production, magnetic fields effectively improve hydrogen yield and substrate conversion efficiency by optimizing the activity of functional microbes, regulating metabolic pathway distribution, and improving mass transfer conditions. In synthesis of high-value chemicals, magnetic fields accelerate the hydrolysis and acidification of organic matter, promote the enrichment of functional microorganisms, and enhance electron transfer, thereby increasing the selectivity and yield of target products. Finally, given the current challenges, such as the insufficient understanding of the underlying mechanisms of MME and the lack of standardized magnetic parameters, this paper proposes future research directions. Emphasis should be focused on multi-omics mechanistic studies, standardization of process parameters, and integrated application with other technologies to advance both theoretical innovation and engineering practice of MME technology in organic waste resource utilization.