For developing the recycling of fruit by-products from kiwano, a polysaccharide was extracted from kiwano (Cucumis metuliferus) peels, namely Cucumis metuliferus peels polysaccharide (CMPP), with the aim of investigating the potential beneficial effects. The composition of polysaccharides was analyzed by chemical methods. RAW264.7 macrophages cells and the microbiota dynamics simulator (BFBL gut model) were used for in vitro study. The result showed that CMPP mainly consists of glucuronic acid, arabinose, galactose and rhamnose. By intervening with RAW264.7 cells, CMPP promoted cell proliferation and showed immune-enhancing activity, which significantly (p < 0.05) induced the release of nitric oxide (NO), tumor necrosis factor α (TNF-α) and interleukin 6 (IL-6) at a concentration of 50 μg/mL. In addition, CMPP had an impact on the composition of the gut bacteria, increasing the growth of Akkermansia, Bacteroides, Bifidobacterium, Feacalibacterium, and Roseburia. During the intake period, acetic, butyric and propionic acids were all increased, especially (p < 0.05) in the descending colon. Moreover, a decrease in ammonia concentration (10.17 ± 0.50 mM in the ascending colon, 13.21 ± 1.54 mM in the transverse colon and 13.62 ± 0.45 mM in the descending colon, respectively) was observed. In summary, CMPP can be considered as a pectin, showed immunological activity and function of gut microbiota modulation. This study could be the scientific basis of developing kiwano peels as beneficial to human health.