A highly efficient technology for the combustion of hard-to-burn agricultural biomass with an annual regeneration cycle has been developed in Ukraine, based on jet-vortex bio-heat generators. The technology enables the combustion of sunflower, rapeseed, wheat, and corn processing residues of various dispersity and with moisture content up to 40%. These heat generators, with capacities ranging from 1.0 to 5.0 MW, have proven their efficiency and are already widely applied, particularly for grain drying and building heating. The cost of thermal energy produced in such bio-heat generators is 5–7 times lower compared to traditional hydrocarbon-based sources. The objective of this study is to improve the environmental performance of a 3 MW vortex heat generator by optimizing biomass mixing and combustion processes through the application of numerical methods. Numerical modeling of biomass particle mixing and combustion processes in the vortex heat generator was performed using the finite volume method. The obtained results revealed shortcomings in the combustion process within the flow path of the existing generator design. The authors propose a novel structural scheme, in which secondary air is supplied at an inclination to the axis of the heat generator. Numerical investigations demonstrated that such an organization of the combustion process reduces the velocity of combustible gas release from biomass particles, enhances the mixing of combustible gases with secondary air, and decreases nitrogen monoxide emissions by 22%.