Food waste can be used more efficiently to increase food sustainability. Polysaccharides from jackfruit peel (PJP) are derived from agricultural waste, and little is known about their in vitro digestion and fermentation characteristics. This study aimed to elucidate PJP structural properties, the dynamic changes during in vitro simulated salivary gastrointestinal digestion and fecal fermentation, and its effects on the human intestinal microbiota. Structural analysis showed a typical polysaccharide structure with high stability in an amorphous heteropolysaccharide. The monosaccharides of PJP are glucose, mannose, galactose, arabinose, and rhamnose. In vitro digestion models, showed that the PJP can reach the colon intact. PJP degradation by the intestinal microbiota being during fecal fermentation, releasing free oligosaccharides, producing short-chain fatty acids, particularly acetic acid, and modulating the composition of intestinal microbes. PJP promoted the growth of beneficial flora Weissella, Enterococcus, Bifidobacterium, Lactococcus and Prevotella during the fermentation process. These findings could improve the usage of jackfruit peel waste, and create possibilities for its use as a potential prebiotic.