Both diet and genetic background have profound effects on plasma lipid profiles. It was hypothesized that a high carbohydrate (high-CHO) diet could affect the ratios of serum lipids and apolipoproteins (apo) differently in subjects with different genotypes of the C-514T hepatic lipase rs1800588 polymorphism. Fifty-six healthy university students were given a stabilization diet of 54.1% carbohydrate for 7 days, followed with a high-CHO diet of 70.1% carbohydrate for 6 days. Body composition, serum lipids, apolipoproteins and the hepatic lipase C-514T rs1800588 polymorphism were analyzed. The ratios of serum lipids and apolipoproteins were calculated afterwards. At baseline, females have significantly lower waist circumference (WC) (CC genotype: p = 0.049; T carriers: p = 0.015) and waist-to-hip ratio (WHR) (CC genotype: p = 0.019; T carriers: p = 0.000) than males. When compared with those before the high-CHO diet, the body mass index (BMI) (p = 0.043) and WC (p = 0.048) were significantly decreased in the male T carriers, the TG/HDL-C ratios were significantly increased in females (CC genotype: p = 0.047; T carriers: p = 0.003). The TC/HDL-C ratios were significantly decreased in males (CC genotype: p = 0.000; T carriers: p = 0.003). And the LDL-C/HDL-C ratios were significantly decreased in all subjects (males with the CC genotype: p = 0.001; male T carriers: p = 0.000; females with the CC genotype: p = 0.018; female T carriers: p = 0.006). However, the apoB100/apoAI ratio was only significantly decreased in male CC genotype after the high-CHO diet (p = 0.005).