Objective To explore the nutritional efficacy of compound protein powder formulations from different sources. Methods Three groups of compound protein powder formulations were obtained through scientific blending using soy protein, whey protein and yeast protein as raw materials. The effects of the compound protein powders on nitrogen metabolism, serum biochemical indicators, and pathological changes of liver tissue and epididymal fat in rats were evaluated. Results Compared with the control (casein), the net protein utilization, biological evaluation, and protein efficacy ratio of the compound protein powders in rats were significantly improved, and the changes in these indicators in the formula with the highest whey protein content were most significant among all three formulas. The compound protein powders effectively increased the levels of albumin and globulin, while decreased the content of total cholesterol, indicating beneficial effects on improving immunity and controlling lipid metabolism, with the formula group 2 being the most effective among all three groups. The pathological examination showed that the three groups of protein powder did not have adverse effects on liver tissue and epididymal fat. Conclusion The present study demonstrates that the compound protein powder formulation has nutritional value, which suggests a potential of the application of the compound protein powder formulation in the elderly, and people with special nutritional needs, such as sports people.