Studies have shown that blue mussel lipid extract (BMLE) can improve the glycemic traits, inflammatory cytokines, and lipid profile of patients with type 2 diabetes mellitus (T2DM) in China. Gut microbiota is closely related to T2DM. This study aims to explore whether BMLE can improve the glycemic status of T2DM patients by regulating gut microbiota in a 60-day double-blind randomized controlled trial. A total of 133 T2DM subjects were randomized into BMLE (n = 44), fish oil (FO) (n = 44), and corn oil (CO) (n = 45) groups. The participants were asked to take two corresponding oil capsules (0.8 g per capsule each) every day. The faecal microbiota, glycemic traits, and other cardiometabolic factors were analyzed at baseline and endpoint. The α diversity estimators of Ace and Chao1 decreased significantly in all three groups, but there was no significant difference between the groups. Eight bacteria decreased significantly in the BMLE group but not in the FO and CO groups: unclassified_Clostridia_UCG_014, unclassified_Bacteroidia, Erysipelotrichaceae, and uncultured_Ruminococcaceae_bacterium at the family level and unclassified_Bacteroidia, uncultured_Ruminococcaceae_bacterium, unclassified_Clostridia_UCG_014, and Turicibacter at genus level. In the BMLE group, the change in the relative abundance of Erysipelotrichaceae was positively correlated with the changes in the homeostatic model assessment of insulin resistance (HOMA-IR) (r = 0.454, p < 0.01) and fasting insulin (r = 0.414, p < 0.01). The change in the relative abundance of Turicibacter was positively correlated with the changes in HOMA-IR (r = 0.431, p < 0.01), fasting insulin (r = 0.414, p < 0.01), total cholesterol (TC) (r = 0.358, p < 0.05), and triacylglycerol (TG) (r = 0.393 p = 0.013). In conclusion, BMLE might improve glycemic traits by modulating gut microbiota in T2DM patients.