To solve the difficulty of storing and transporting yak butter, yak butter microcapsule powders were prepared using a mixture of maltodextrin and sodium caseinate as the wall material, a mixture of molecular distilled monoglycerides and sucrose ester as the emulsifier and guar gum as the stabilizer by vacuum freeze-drying or spray drying. The basic physicochemical properties (moisture content, solubility, rheology, surface oil content, encapsulation efficiency, and yield), microscopic structure, and thermal stability of the two as-prepared samples were compared. The results showed that the microencapsulated powders prepared by the two methods were milky white in color and free of impurities, and had a fresh aroma. Both of them exhibited high encapsulation efficiency, (90.17 ± 1.07)% and (92.12 ± 0.32)%, respectively. The yield of freeze-dried microcapsule powders, (98.42 ± 0.38)%, was significantly higher than that of spray-dried microcapsule powders, (25.77 ± 1.34)%, and the average particle size (D_[4,3] = 16.695 μm) was smaller than that of spray-dried powder (D_[4,3] = 24.945 μm). The solubility and fluidity of the spray-dried powder were superior to those of the freeze-dried powder. Under a scanning electron microscope (SEM), the surface of spray-dried powder was smooth and spherical in shape, while the freeze-dried powder was irregular. The thermal stability of the spray-dried powder was better. In summary, when considering economic benefits, the spray-dried powder holds greater significance for industrial production.