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Biomass combustion, as a key technology for achieving a low-carbon transformation of the energy system, faces multiple challenges in its efficient and clean utilization, including the high heterogeneity of fuels, the complex multi-scale coupling of the combustion process, and the attainment of ultra-low emissions. Traditional research methods have significant disconnections between microscopic mechanism understanding, macroscopic performance prediction of reactors, and end-of-pipe pollution control, which restricts the improvement of system performance. This review presents recent advances in advanced numerical simulation, pollutant control strategies, and bioenergy with carbon capture and storage (BECCS) pathways targeting ultra-low emissions in biomass combustion. This work synthesizes progress across three interconnected domains. First, methodologies are examined for integrating detailed chemical kinetics, particle-scale models, and reactor-scale simulations to develop high-fidelity predictive tools. Second, low-nitrogen combustion and synergistic pollutant control strategies for primary furnace types (e.g., grate, fluidized bed) are evaluated, alongside process optimization from fuel pretreatment to flue gas purification. Third, the potential for integrated design of biomass energy systems with carbon capture is assessed, emphasizing that system efficiency hinges on holistic “fuel-combustion-capture” chain optimization rather than isolated unit improvements. Future research directions are highlighted, including the development of physics-informed AI modeling paradigms, deeper co-design of multiple processes, and the establishment of robust life-cycle assessment frameworks. This review aims to provide a structured reference to inform both fundamental research and the practical development of next-generation clean biomass combustion technologies.