This study aimed to investigate the protective effect of mussel polysaccharide (MP) on cyclophosphamide (Cy)-induced intestinal mucosal immunosuppression and microbial dysbiosis in mice. MP was shown to stimulate secretion of cytokines (SIgA, IL-2, IF-γ, IL-4, IL-10) and production of transcription factors (occludin, claudin-1, ZO-1, mucin-2, IL-2, IF-γ, IL-4, IL-10). Key proteins (p-IκB-α, p-p65) of the NF-κB pathway were upregulated after MP administration. SCFAs levels, which were decreased after the Cy treatment, were improved after treatment with MP. Furthermore, 16 S rRNA sequencing data of fecal samples revealed, through α-diversity and β-diversity analysis, that MP improved microbial community diversity and modulate the overall composition of gut microbiota. Taxonomic composition analysis showed that MP increased the abundance of probiotics species (Lactobacillus) and decreased the proportion of pathogenic species (Desulfovibrio). These findings suggested that MP has a potential immunomodulatory activity on the immunosuppressive mice.