Objective To evaluate the clinical characteristics and surgical treatment effectiveness of blood culture-negative infective endocarditis (IE). Methods Clinical data of patients with IE who underwent surgical treatment in department of cardiothoracic surgery of a hospital from January 2014 to December 2021 were collected, patients were divided into positive group and negative group according to the results of blood culture pathogen, clinical characteristics and surgical treatment effectiveness of two groups of patients were analyzed retrospectively. Results A total of 88 patients were with IE, 61 of whom were negative for blood culture (negative group) and 27 were positive for blood culture (positive group), with a positive rate of 30.7%. 83 patients were found positive by echocardiography before operation, including vegetations, valve damage, perivalvular leakage of artificial valve, abscess, rupture of chordae tendineae, etc, all patients were treated by surgery. The ratio of fever in negative group was lower than that in positive group (36.1% vs 81.5%), the ratio of chest tightness and shortness of breath was higher than that in positive group (80.3% vs 74.1%), difference was significant (all P < 0.05). In 61 patients in negative group, the primary heart disease was mainly associated with bicuspid aortic valve malformation (16.4%); involving aortic valve (n=37), mitral valve (n=20) and tricuspid valve (n=2), 2 cases involving both aortic valve and mitral valve, proportion of valve deterioration and rupture of chordae tendineae were both higher than positive group (78.7% vs 63.0%, 47.5% vs 22.2%), difference were both significant (both P < 0.05). The main complications of both groups of patients were cardiac insufficiency and embolism; 18 patients with cardiac insufficiency were in negative blood culture group, incidence was 29.5%, and 7 patients were in positive blood culture group, incidence was 25.9%. Mortality of patients in negative group and positive group were 8.2% and 7.4% respectively, there was no significant difference between two groups (P>0.05). Conclusion Early diagnosis, early standardized treatment, selection of appropriate surgical opportunity and scheme, and strengthening perioperative management can achieve better therapeutic effect for IE patients with negative blood culture.