Stress exposure can increase the appearance of intestinal dysfunction. DHA and EPA have been shown to possess significant anti-inflammatory and immuno-enhancement bioactivities. The aim of the study was to investigate whether different forms of DHA or EPA would affect intestinal barriers (including intestinal epithelium integrity and immunity responses, gut microbiota and its metabolites) in mice under chronic stress, and might therefore prevent stress induced intestinal dysfunction. Chronic stress caused a series of anomalies in the intestine, including decreased faecal water content, increased pro-inflammatory cytokines (IFN-γ, TNF-α, IL-1β and IL-6), reduced expression levels of ZO-1, occludin and E-cadherin, and aberrant microbiota composition (especially Roseburia spp., Prevotella spp., bifidobacteria and lactobacilli) and its metabolites, mainly LPS, acetic acid, propionic acid and butyric acid. Our data indicated that both DHA-PL and EPA-PL counteracted these adverse effects effectively. In conclusion, DHA-PL and EPA-PL may effectively protect mice against intestinal dysfunction under chronic stress exposure as potential ingredients for functional food.