Using the data of China National Nutrition and Health Survey, we explored the relationship between dietary fructose intake and lipid indexes and dyslipidemia of 27 265 Chinese residents aged 45 and above. The level of serum total cholesterol (TC), triglycerides (TG) and high-density lipoprotein Cholesterol (HDL-C) were significantly lower in male while dietary fructose intake was lower in female (P < 0.001). With the increase of the dietary fructose quartile level, serum TG concentration was increased while HDL-C was decreased for male residents (Ptrend < 0.001). Among female residents, we only found serum TG concentration was increased (Ptrend < 0.001). Compared with the first quartile, the risk of low HDL cholesterolemia in the third (OR: 1.17; 95%CI: 1.03~1.33) and fourth (OR: 1.25; 95%CI: 1.08~1.43) quartile were increased after adjustment for confounding factor. There was no association between dietary fructose intake and hypercholesterolemia, hypertriglyceridemia, mixed hyperlipidemia, and dyslipidemia among female residents after adjustment for confounding factor (P > 0.001). There were gender differences for the effect of dietary fructose intake on lipid indexes and dyslipidemia.