The ability of a combination of enzymatic fragments of Porphyra polysaccharides of different molecular weights and oyster peptides to synergistically reduce exercise fatigue was investigated. Mice were randomly divided into a normal group (N), an exercise group (M), an oyster peptide intervention group (O), and combined intervention groups jointly treated with oyster peptides and high-, medium-, and low-molecular-weight enzymatic fragments of Porphyra polysaccharides (OH, OM, and OL). All groups received continuous intervention for 16 d. Compared with oyster peptide intervention alone, interventions combining enzymatic fragments of Porphyra polysaccharides and oyster peptides yielded superior anti-fatigue activity. In the OH, OM, and OL groups, swimming endurance times increased by 60.77%, 37.25%, and 37.59%, respectively. In the OH group, liver AST and ALT levels decreased by 12.88% and 11.39%, respectively. Serum CK and LDH activities were significantly reduced by 22.02% and 8.99%, respectively, suggesting that exercise-induced liver and skeletal muscle damage was reduced. Liver glycogen content also increased in the intervention groups, whereas serum lactate and urea nitrogen levels decreased, indicating reduced oxidative stress levels. Mechanism analysis revealed that a combination of enzymatic fragments of Porphyra polysaccharides with oyster peptides synergistically upregulated PGC1α/TFAM signaling in skeletal muscle, increased the abundance of beneficial Lactococcus bacteria, and decreased the abundance of pathogenic bacteria, including Staphylococcus, Acinetobacter, Oscillospira, and Ruminococcus. In conclusion, a combination of enzymatic fragments of Porphyra polysaccharides with oyster peptides can synergistically ameliorate exercise fatigue in mice by promoting mitochondrial biogenesis and regulating gut microbiota. High-molecular weight enzymatic fragments of Porphyra polysaccharides (Mw=267.3 ku) exhibited the best efficacy. This study provides a theoretical basis for the development of Porphyra-based health products.