The objective was to examine the change of metabolites in response to omega‐3 fatty acid supplementation in Chinese diabetic patients. Fifty‐nine patients with type 2 diabetes were randomized into three groups: fish oil (FO, n=20, 50% of C20:5n‐3+C22:6n‐3), flaxseed oil (FLO, n=20, 63% of C18:3n‐3) and corn oil (CO, n=19). The patients consumed corresponding capsules (4 capsules/d) for 6 months. Seventeen healthy subjects without diabetes were recruited as healthy controls (HC) for metabolomic analysis. At baseline, plasma C20:5n‐3 and C22:6n‐3 were significantly lower in diabetic patients compared with HC ( P <0.05). FO supplementation significantly increased plasma C20:5n‐3 and C22:6n‐3 ( P <0.05), while FLO supplementation significantly increased plasma C18:3n‐3 ( P <0.05), compared with CO. In addition, FO intake significantly increased sterol metabolites campesterol and beta‐sitosterol compared with CO ( P <0.05). Baseline furan fatty acid metabolite 3‐carboxy‐4‐methyl‐5‐propyl‐2‐furanpropanoate (CMPF) was significantly lower in diabetic patients compared with HC, while FO supplementation significantly increased plasma CMPF. Baseline plasma C20:5n‐3 was positively correlated with CMPF (r=0.44, P =0.001). In conclusion, fish oil supplementation may have beneficial effects on diabetic patients by increasing tissue n‐3 fatty acid compositions and regulating sterol and furan fatty acid metabolites.