Matrix metalloproteinase-9 (MMP-9) has been shown to participate in the pathogenesis of sepsis. In this study, we recruited 312 sepsis patients and 413 controls to explore the relationship between sepsis risk and the MMP-9 -1562 C/T polymorphism in Han Chinese. The PCR restriction fragment length polymorphism method was used for genotyping. Our data indicated that the MMP-9 -1562 C/T polymorphism was related with the risk of sepsis (CT vs. CC: P = 0.033, odds ratio (OR) = 1.45, 95% confidence interval (CI) 1.03–2.05; TT+CT vs. CC: P = 0.019, OR = 1.49, 95% CI 1.07–2.07). Stratified analyses demonstrated that this effect was more evident in smokers, drinkers, females and overweight individuals. Furthermore, cross-over analyses suggested that the combined effect of smoking and CT genotype of -1562 C/T polymorphism contributed to the risk of sepsis. In addition, MMP-9 serum levels were significantly lower in sepsis patients than in controls. The MMP-9 -1562 C/T polymorphism was significantly associated with decreased MMP-9 serum levels. Lastly, we observed that this polymorphism was connected to the mortality of sepsis. In conclusion, the interaction between the MMP-9 -1562 C/T polymorphism and smoking correlated with the risk of sepsis in Han Chinese. This polymorphism may serve as a diagnostic marker for sepsis patients.