Ulcerative colitis recently has become an increasingly common disease worldwide, mainly due to people’s unbalanced daily diets. The effects of three different marine lipids, namely eicosapentaenoic acid (EPA), docosapentaenoic acid (DPA) and docosahexaenoic acid (DHA), on ulcerative colitis mice and influences on their intestinal flora were studied. In the present study, the C57BL/6 mice were used as experimental model, induced by dextran sulfate sodium (DSS); The protective effects of these three kinds of marine lipids on ulcerative colitis were evaluated by the indexes of the body weight loss, disease activity index (DAI) score, the morphology of colon, the length of colon, the ratio of colon weight to length, the microscopic images of colon sections stained with hematoxylin-eosin (H.E) and histological damage score; 16S rDNA high-throughput sequencing method was adopted to characterize the influences of these three marine lipids on the microecological changes of intestinal flora in mice. DAI of EPA, DPA, DHA and model group increased 0.33-3.33, 0.33-2.67, 0-3.00, 0.33-4.00 respectively; length of colon tissue increased by 21.12%, 21.90% and 22.29% in EPA, DPA and DHA group compared to model mice (5.16 cm); the ratio of colon weight to length of EPA, DPA and DHA group reduced by 22.18%, 22.15% and 24.55% compared with model mice; mice treated with EPA, DPA and DHA showed lower histological damage score (2.51, 2.16, 2.23 respectively) while DSS treated mice showed worse intestinal morphology (3.51). The results of pathological indexes showed that the decrease of body weight, the increase of DAI, the shortening of the colon tissue and the increase of histological damage score were significantly inhibited by the supplementation with these three kinds of marine lipids, compared with the model group. Moreover, DPA was more effective in the prevention of the loss of body weight, the increase of disease activity index score and the increase of the histological damage score than EPA and DHA. Higher abundance of Akkermansia, Alistipes, Bifidobacterium, Blautia, Butyricicoccus, Eubacterium and Oscillibacter and lower abundance of Allobaculum, Bacteroides, Desulfovibrio, Enterococcus, Esherichia/Shigella, Lactococcus, Prevotella and Lachnospiraceae were showed in mice treated with EPA, DPA and DHA by 16S rDNA high-throughput sequencing, compared with the model group. The results represented the significantly regulatory effect of these three kinds of marine lipids on intestine flora ecology. In addition, DPA was more effective in the regulation of the relative abundance of Akkermansia, Alistipes, Butyricicoccus and Esherichia/Shigella, compared with EPA and DHA. All these findings indicated that EPA, DPA and DHA, these three kinds of marine lipids could significantly alleviate the symptoms of UC, and the composition and structure of intestinal flora in UC mice were significantly affected by the supplementation of these three kinds of marine lipids. Based on these, we assumed that the regulation effect of these three kinds of marine lipids on UC was related to their regulation effect on the specific intestinal microorganisms. We hope this study could provide important reference for the research of biological effects of marine active lipids, especially for the biological effects of DPA. Moreover, we hope this study could also provide important reference for the dietary control of chronic diseases.