Objective To investigate the clinical characteristics and risk factors of postoperative venous thromboembolism (VTE) in patients after thoracoscopic surgery. Methods Clinical data of the patients who underwent video-assisted thoracic surgery (VATS) in our hospital from January 2014 to August 2020 were collected and analyzed retrospectively. The demographic characteristics, surgery related data and length of hospital stay were collected and compared between the VTE patients and those without, cumulative incidence rate of VTE in different ages, body mass index (BMI), and operation time were analyzed. SPSS statistics 28.0 was used for statistical analysis. Data comparison between two groups was performed using U test, Chi-square test or Fisher exact test depending on data type. Results A total of 21 227 patients who underwent minimally invasive surgery were enrolled in this study. In the 17 213 patients who underwent laparoscopic surgery, the incidence of VTE was 0.43% (74/17 213). In 2 133 patients who underwent VATS, VTE occurs in 1.22% (26/2 133), and deep vein thrombosis (DVT) covered 34.62% (9/26), while pulmonary thromboembolism (PTE) covered 65.38% (17/26). Compared with the non-VTE group, older age [65 (60,73) vs 54 (43,62) years, P<0.001], larger BMI [25.46 (24.61,28.67) vs 23.83 (21.51,26.03) kg/m², P<0.001], higher incidence of malignancy [22(84.62%)vs 1203(57.10%),P=0.005] and longer operation time [165 (119,214) vs 95 (67,134) min, P<0.001] and length of hospital stay [10 (8,18) d vs 6 (4,7) d, P<0.001] were observed in the VTE group. When the VATS patients were divided into four aged groups:<60,60-<65,65-<70, and ≥70 years, and the incidence of VTE was 0.43% (6/1 391), 1.75% (6/342), 2.12% (5/236), and 5.49% (9/164), respectively. Independent risk factors for VTE occurrence after VATS included ≥65 years old (OR=2.917, 95%CI 1.253-6.788, P=0.013), BMI >25 kg/m²(OR=2.484, 95%CI 1.089-5.667, P=0.031), and operation time≥120 min (OR=4.683, 95%CI 1.762-12.241, P=0.002). Compared with patients <65 years old, BMI≤25 kg/m², and operation duration <120 min, the incidence of VTE within 30 d after VATS was higher in patients≥65 years old [9/164(5.49%) vs 17/1969(0.86%), P<0.001], BMI>25 kg/m²[15/757(1.98%) vs 11/1376(0.80%), P=0.012] and operation duration≥120 min [2.86%(20/699) vs 0.42%(6/1 434), P<0.001]. Conclusion The incidence of postoperative VTE is higher in patients who underwent VATS than laparoscopic surgery in Peking Union Medical College Hospital. Age ≥65 years, BMI >25 kg/m² and operation time longer than 120 min are the independent risk factors of the incidence of VTE in patients after undergoing thoracoscopic surgery.