Royal jelly has the function of delaying aging and has a certain protective effect on kidney damage caused by various conditions. However, it is not clear whether royal jelly also has an effect on age-related kidney function decline. To study the effect of royal jelly on the kidneys of aging mice, SPF Kunming mice were used as the research subjects. Fifty mice (equal number of females and males) were divided into 5 groups. The control group was injected and gavaged with normal saline, while the other four groups were injected with D-galactose to establish a mouse aging model. Meanwhile, the aging model group was gavaged with normal saline, two positive control groups were gavaged with vitamin E and Liuwei Dihuang pills, respectively, and the experimental group was gavaged with royal jelly. The experiment lasted for 90 days. The kidney function was evaluated through kidney index, kidney histopathological sections, and the levels of blood urea nitrogen and creatinine. The total antioxidant capacity and superoxide dismutase levels were used to evaluate the tissue's antioxidant capacity. Untargeted serum metabolomics were performed to identify the main metabolites and metabolic pathways regulated by royal jelly. The results showed that there were significant changes in the kidneys of aging mice, with significant dilation of the renal capsule and atrophy of the glomerular. The blood urea nitrogen and creatinine levels in the aging mice significantly increased, while the total antioxidant capacity and superoxide dismutase levels significantly decreased. However, feeding with Vitamin E, Liuwei Dihuang pills, and royal jelly alleviated the decline in kidney physiological function and antioxidant capacity to varying degrees. Royal jelly and Liuwei Dihuang pill groups exhibited better protection for the kidney disease caused by aging. Serum metabolomic results of aging mice showed that compared to the Liuwei Dihuang pills group, royal jelly had more targeted regulation on metabolism, mainly involved in amino acid metabolism, energy metabolism, and lipid metabolism. Compared to the model group, total 308 and 343 significant changed metabolites were found and enriched in 19 and 15 metabolic pathways in female and male mice of royal jelly groups, respectively. These metabolic pathways were mainly associated with antioxidation, improved energy supply, and maintenance of basic kidney functions. The results indicated royal jelly had certain protective effect on the kidneys of D-galactose induced aging mice and would provide a theoretical basis for the further development of royal jelly as a functional food.