Abstract: Non-targeted metabolomics techniques were used to analyze the metabolite differences in the calyx, fruit, stem, and root of Physalis alkekengi L. var. franchetii (PAVF). The metabolomic profiles of PAVF were investigated by UHPLC-Q-Orbitrap HRMS with PCA, OPLS-DA, HCA, and metabolite and metabolic pathway difference analysis. The results showed that 1416 metabolites were detected, with the highest proportion of organic acids, alkaloids, and amino acids and their derivatives. The results of multivariate statistical analysis showed that there were significant differences amongst different parts of PAVF. The calyx contained high flavonoids, phenylpropanoids, and vitamins. The fruit contained high organic acids, alkaloids, and steroids. The stem contained high terpenes, flavonoids, esters, and phenolic acids. The root contained high sugars, lipids, and amino acids and their derivatives. OPLS-DA analysis identified 113 differential metabolites (VIP>1.7 and P<0.05), with the highest proportion of organic acids, alkaloids, and lipids, which were mainly involved in the metabolic pathways of unsaturated fatty acid biosynthesis, citrate cycle, and pyruvate metabolism. Twenty percent of the flavonoids identified were differential metabolites, and such components had the largest proportion of variation among differential metabolites. This study may provide a theoretical reference for the composition differences and efficient resource utilization of PAVF.