Artocarpus heterophyllus Lam. is rich in nutrients, including carbohydrate, protein, amino acid, polyphenol, fatty acid, vitamin and minerals, which can be used as good sources for some important nutrients. Nowadays, A. heterophyllus Lam. trees are widely distributed in Hainan, Guangdong, Guangxi, Yunnan, Fujian, and Taiwan provinces. Polysaccharide, as an important biological molecule, participates in cell activities. Recently, a water-soluble polysaccharide named JFP-Ps was isolated from A. heterophyllus Lam. pulp, which consisted of rhamnose, arabinose, galactose, glucose, xylose and galacturonic acid, with an average molecular weight of 1668 kDa. JFP-Ps exerted immunomodulatory effect by inducing lymphocyte proliferation, enhancing antioxidant activity and increasing the secretion of TNF-α, IFN-γ and IL-1β. Moreover, JFP-Ps can be fermented into short-chain fatty acids, including acetate, propionate, butyrate and valerate acid by gut microbiota. However, there was little research about the the metabolism of JFP-Ps during gastrointestinal digestion. Based on our previous research, the present study was aim to investigate the fecal metabolomics of JFP-Ps on fecal metabolites from mice. Healthy Kunming mice were divided into four groups, including 50 mg/kg mouse body weight (low dose group), 100 mg/kg mouse body weight (medium dose group), and 200 mg/kg mouse body weight (high dose group) and the same volume of distilled water (blank control group). After experimental treatment for 2 weeks, fresh fecal samples were collected for metabolomics analysis. A metabolomics method based on Agilent 1290 series UPLC and with 6530B series Q-TOF mass spectrometer (UPLC-Q-TOF-MS/MS) was developed to identify the fecal metabolites. Then related metabolic pathways were analyzed by matching KEGG and Wiki pathways. Our results showed that 30 potential biomarkers were authenticated using principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA), including 22 types in the negative ion mode and 8 characteristic metabolites in the positive ion mode. The results of metabolomics pathway analysis showed that the metabolites were related to the biological pathways and processes, including metabolism of phenylalanine, alanine, aspartic acid, tryptophan, cholesterol, 2-oxocarboxylic acid and nucleotide. They also have been proven to be related to the tricarboxylic acid cycle activity, PPAR signaling pathway, activation pathways in class A GPCRs, degradation of benzoic acid and derivatization of amino acids, nuclear receptors, glutathione and one-carbon cycle, urea cycle and amino metabolism pathways. The results indicated that JFP-Ps could regulate the metabolism of cholesterol, biosynthesis of fatty acid and triglycerides, omega-3 and omega-6 fatty acids metabolism and the secondary metabolites in mice. The results could provide theoretical basis for elucidating the bioactive substances and its mechanism of JFP-Ps.