Objective To explore the relationship between apolipoprotein B (ApoB) gene MspⅠ/XbaⅠ/EcoRⅠ polymorphisms and the levels of serum lipid in male Han population in Chongqing. Methods The ApoB gene MspⅠ/XbaⅠ/EcoRⅠpolymorphisms were detected by gene chip technology in 157 dyslipidemia cases and 180 healthy controls; and their relationship with serum lipids was analyzed in the dyslipidemia group and the controls. Results In both dyslipidemia group and control group, the total cholesterol (TC) levels with M⁺M^- genotype at MspⅠ locus were significantly higher than those with M⁺M⁺ genotype (dyslipidemia group: [6.54±0.58] vs [5.58±0.83] mmol/L, P<0.01; control group: [5.43±0.17] vs [4.39±0.62] mmol/L, P<0.01); the high density lipoprotein cholesterol (HDL-C) levels with X⁺X^- genotype at XbaⅠ locus were significantly lower than those with X^-X^- genotype, whereas the low density lipoprotein cholesterol (LDL-C) levels were significantly higher than those with X^-X^- genotype (dyslipidemia group HDL-C: [1.08±0.27] vs [1.22±0.44] mmol/L, P=0.03; LDL-C: [3.88±0.63] vs [3.46±0.83] mmol/L, P=0.01; control group HDL-C: [1.31±0.43] vs [1.48±0.37] mmol/L, P=0.04; LDL-C: [3.19±0.54] vs [2.94±0.59] mmol/L, P=0.02); the HDL-C levels with E⁺E^- genotype at EcoRⅠ locus were significantly lower than those with E⁺E⁺ genotype (dyslipidemia group: [1.01±0.18] vs [1.21±0.43] mmol/L, P=0.01; control group: [1.27±0.20] vs [1.47±0.40] mmol/L, P=0.03). The HDL-C levels in dyslipidemia group with X⁺X^- genotype were significantly lower than the control group with X⁺X^- genotype, but the LDL-C levels were significantly higher than the control group with X⁺X^- genotype (HDL-C: [1.08±0.27] vs [1.31±0.43] mmol/L, P=0.01; LDL-C: [3.88±0.63] vs [3.19±0.54] mmol/L, P<0.01); the HDL-C levels in the dyslipidemia group with E⁺E^- genotype were significantly lower than those in the control group ([1.01±0.18] vs [1.27±0.20] mmol/L, P<0.01). The multiple linear regression analysis showed that ApoB gene MspⅠ polymorphism was positively correlated with TC; XbaⅠpolymorphism was negatively correlated with HDL-C and positively correlated with LDL-C. Conclusion The ApoB gene MspⅠ and XbaⅠ polymorphisms may be associated with the levels of serum lipids. There is a tendency that the M⁺M^- genotype can increase TC levels and the X⁺X^- genotype can reduce HDL-C levels and increase LDL-C levels.