The present study aimed to investigate the effects of n-3 fatty acid supplements on urine metabolite profiling and their correlation with metabolic risk factors in Chinese T2D patients. A double-blind randomized controlled trial was conducted in 59 Chinese patients with T2D, who were randomized to receive fish oil (FO), flaxseed oil (FSO) or corn oil (CO, serving as a control group) capsules for 180 days. Morning urine samples were collected before and after the intervention and were analyzed for metabolomics by UHPLC-Q-Exactive Orbitrap/MS in positive and negative ionization modes. In the FO group, levels of 2-hexenoylcarnitine (C6:1) (p < 0.001) and 3-carboxy-4-methyl-5-propyl-2-furanpropanoic acid (CMPF) (p = 0.004) were significantly increased while hydroxyisovaleroyl carnitine (C5:OH) (p < 0.001) was significantly decreased compared with the CO group. In addition, geranylacetone (p = 0.023) and citronellyl propionate (p = 0.038) levels were significantly elevated, while dihydrojasmonic acid (p = 0.003) was significantly reduced in the FSO group compared with that in the CO group. Moreover, increased C6:1 was correlated with decreased serum triglycerides (r = -0.340, p = 0.020). The change of urine CMPF showed inverse correlation with blood urea nitrogen (BUN) (r = -0.338, p = 0.020), while C5:OH was positively correlated with apolipoprotein B (APOB) and BUN (r = 0.386, p = 0.015; r = 0.327, p = 0.025). Besides, the change of urine CMPF was positively correlated with serum CMPF (r = 0.646, p < 0.001). In conclusion, the present study confirmed that CMPF is a strong biomarker of fish oil, and indicated that marine n-3 PUFA intake might have a beneficial effect on lipid metabolism and renal function in patients with T2D.