The gut microbiota is important in regulating host metabolism, maintaining physiology, and protecting immune homeostasis. Gut microbiota dysbiosis affects the development of the gut microenvironment, as well as the onset of various external systemic diseases and metabolic syndromes. Cyclophosphamide (CTX) is a commonly used chemotherapeutic drug that suppresses the host immune system, intestinal mucosa inflammation, and dysbiosis of the intestinal flora. Immunomodulators are necessary to enhance the immune system and prevent homeostasis disbalance and cytotoxicity caused by CTX. In this study, shrimp peptide hydrolysate (SPH) was evaluated for immunomodulation, intestinal integration, and microbiota in CTX-induced immunosuppressed mice. It was observed that SPH would significantly restore goblet cells and intestinal mucosa integrity, modulate the immune system, and increase relative expression of mRNA and tight-junction associated proteins (Occludin, Zo-1, Claudin-1, and Mucin-2). It also improved gut flora and restored the intestinal microbiota ecological balance by removing harmful microbes of various taxonomic groups. This would also increase the immune organs index, serum levels of cytokines (IFN-ϒ, IL1β, TNF-α, IL-6), and immunoglobin levels (IgA, IgM). The Firmicutes/Bacteroidetes proportion was decreased in CTX-induced mice. Finally, SPH would be recommended as a functional food source with a modulatory effect not only on intestinal microbiota, but also as a potential health-promoting immune function regulator.