Flammulina velutipes residues, the by-products of Flammulina velutipes industry, cause environmental pollution. The aim of the current work was to evaluate the extraction efficiency of polysaccharides from Flammulina velutipes residues by an ultrasonic assisted snailase enzymatic extraction (UAEE) method, following the principles of green chemistry, mainly solvent and energy saving. The optimized parameters obtained by Response Surface Methodology (RSM) were determined as follows: ultrasonic power at 150 W, extraction time of 90 min, and extraction temperature of 55 °C. The experimental extraction yield (109.54 ± 5.44 mg/g) was closely matched the predicted yield (110.92 mg/g). Polysaccharides from Flammulina velutipes residues (UE-FVRP) had the molecular weight of 170 kDa and a composition comprising 8 monosaccharides, primarily xylose (Xyl, 24.71%), mannose (Man, 17.29%), arabinose (Ara, 11.48%), and galactose (Gal, 15.63%). FT-IR analysis suggested that UE-FVRP likely contained pyranose with α-glycoside bonds. In vitro antioxidant activity assays revealed that UE-FVRP displayed potent DPPH radical scavenging activity and reducing ability. Additionally, UE-FVRP demonstrated the ability to promote the growth of two Lactobacillus strains, indicating its potential as a novel polysaccharide with high in vitro prebiotic properties. Therefore, these findings proposed a novel, green, and efficient extraction method for extracting polysaccharides from Flammulina velutipes residues, highlighting the potential of utilizing Flammulina velutipes residues as a valuable ingredient in both food and feed applications, contributing to the sustainable reuse of agricultural by-products.