Objective To investigate the effect of native-valve infective endocarditis (IE) on long-term effect of surgical aortic valve replacement (SAVR). Methods Medical records of patients with native-valve IE who underwent SAVR in Beijing Anzhen Hospital, Capital Medical University from January 2013 to December 2017 were analyzed retrospectively, propensity score matching (PSM) was adopted to select patients as control group (non-IE), all patients were followed up for a long period to observe the post-operative survival rate and cumulative risk of complications, the median follow-up time was 69 months. Results A total of 2 821 patients were included in study, including 143 SAVR patients with IE (IE group) and 2 678 SAVR patients without IE (control group). The long-term survival rate of patients in IE group was lower than that of control group, difference was significant (P=0.044). Patients with IE were more likely to have ischemic stroke after SAVR, difference was significant (P=0.035), ischemic stroke was an independent risk factor affecting the survival of patients (P=0.014), patients with ischemic stroke had a higher risk of death (HR=2.811; 95% CI: 1.233-6.408). There was no significant diffe-rence in the cumulative incidence of massive hemorrhage and aortic valve re-operation rate between patients in IE group and control group (both P>0.05), and they were not independent risk factors affecting the survival of patients (all P>0.05). Conclusion Compared with patients in control group, patients with native-valve IE have a higher risk of death and ischemic stroke after SAVR. The close follow-up of IE patients after SAVR should be strengthened, focusing on the prevention of complications of stroke.