To determine the effects of plant-based meat analogues on the metabolic health and the possible mechanisms, mice were fed with a real pork diet (AP), a real beef diet (AB), a plant-based pork analogue diet (PP) and plant-based beef analogue diet (PB) for 68 days. Compared with real meat, the plant-based meat analogues increased food and energy intake, body weight, white fat and liver weight and caused adipocyte hypertrophy, hepatic lipid droplet accumulation, and inflammatory responses in mice. Metabolomics revealed that plant-based meat analogues altered the composition of serum metabolites, which regulated lipid metabolism homeostasis. The PB diet upregulated gene expression related to lipid synthesis, lipolysis and adipocyte differentiation while the PP diet upregulated expression of lipolysis-related genes but downregulated expression of adipocyte differentiation-related genes in white adipose tissue. Meanwhile, both PP and PB diets upregulated lipid influx- and synthesis-related genes but downregulated lipid oxidation-related genes in liver. The specific metabolite biomarkers may affect fat accumulation mainly by direct lipid metabolism pathways or indirect amino acid metabolism, protein digestion and absorption, bile secretion, aminoacyl-tRNA biosynthesis, neuroactive ligand-receptor interaction and ABC transporters pathways. These findings provide a new insight into understanding the differences in nutritional functions of meat and plant-based meat analogues.