Whole-body vibration (WBV) can improve skeletal muscle function in aging mice, but whether the effect on young and aging skeletal muscle is consistent has not been studied. We selected C57BL/6J mouse models, which were divided into young control group (YC), young vibration group (YV), aging control group (AC) and aging vibration group (AV). After 12 weeks of WBV, we found that compared with the YC group, the pathways of linoleic acid metabolism, biosynthesis of unsaturated fatty acids, arachidonic acid metabolism, nicotinate and nicotinamide metabolism, glycine, serine and threonine metabolism, and arginine and proline metabolism improved significantly in the YV group. Compared with the AC group, the pathways of arachidonic acid metabolism, alpha-linolenic acid metabolism, biosynthesis of unsaturated fatty acids, pentose and glucuronate interconversions and pentose phosphate pathway improved significantly in the AV group. Furthermore, we found that WBV decreased triglyceride (TG), total cholesterol (TC), and free fatty acid (FFA) levels in aging mice, improved mitochondrial membrane potential, and increased the expression of phosphorylated activated protein kinase (p-AMPK), peroxisome proliferator-activated receptor coactivator-1α (PGC-1α) and carnitine palmitoyl transferase 1B (CPT1B) in the skeletal muscle of young and aging mice. Our study revealed that WBV mainly improved lipid metabolism and amino acid metabolism pathways of skeletal muscle in young mice and mainly improved lipid metabolism and glucose metabolism pathways of skeletal muscle in aging mice. WBV can activate the AMPK/CPT1 signaling pathway and improve mitochondrial function in skeletal muscle in both young and aging mice.