The elderly usually suffer from many diseases. Improving the quality of life of the elderly is an urgent social issue. In this present study, D-galactose treated aging mice models were used to reveal the effects of different animal sources and different doses of whey protein (WP) on the immune indexes organs and intestinal flora. A total of 9 groups were set up, including normal control (NC), negative control (NS), positive control (Vc), low-, medium- and high-doses of cow WP intervention groups (CL, CM and CH for short, correspondingly) and low-, medium- and high-doses of goat WP intervention groups (GL, GM and GH for short, correspondingly). The body weight gain, thymus/body weight ratio, superoxide dismutase (SOD) activity, malondialdehyde (MDA) content, spleen immunoglobulins G (IgG), spleen interleukin-2 (IL-2) and spleen interleukin-2 (IL-6) were measured. Then, the intestinal contents were collected, and 16s genes of intestinal bacteria were sequenced to reveal the changes in bacterial flora structure. WP intervention significantly increased the weight gain, thymus/body ratio and SOD activity, but decrease the content of MDA. WP intervention increased some immune indicators. All the WP treated aging mice showed similar values of physiological indexes to that of the Vc group, even better. The relative abundance of Lactobacillus and Stenotrophomonas was increased and decreased, respectively, by both cow and goat WP. Lactobacillus may be involved in regulating the functional repair of organisms. In contrast, Stenotrophomonas might play a negative role in the immune and antioxidant capacity of the body. Combining physiological indicators and intestinal flora structure, low-concentration WP for cow and goat might be optimal for aging models.