Facing the global shortage of protein resources, yeast protein (YP) has emerged as a sustainable alternative to dietary proteins. This study employed a weaned SD rat model to evaluate the quality of YP by comparing plant-based protein sources and animal-derived protein. Supplementation of YP with whey protein isolate (WPI) or soybean protein isolate (SPI) achieved body weight gains comparable to those of casein. The tryptophan (Trp) in YP was the amino acid with the highest content in true ileal digestible (TID), accounting for 99.92%. Significant enhancements (p < 0.05) in true digestibility (TD) were observed when YP was mixed with SPI or WPI at optimized ratios. Formulation of different protein sources was shown to synergistically enhance DIAAS values. These findings revealed that YP was an ideal protein choice for individuals with Trp and His deficiencies, and partial replacement of animal and plant proteins with YP could enable more balanced amino acid provision.