Background: Predicting the progression of acute pulmonary embolism to chronic pulmonary thromboembolism (CPTE) disease is essential to monitoring and improving the long-term prognosis of pulmonary embolism. We explored the risk Factors for chronic persistence of thromboembolism after acute pulmonary embolism. Methods: Cases with newly onset acute pulmonary embolism in the China-Japan Friendship Hospital from November 2016 to November 2019 were retrospectively analyzed. The clinical characteristics, serological examination results, and treatment strategies of acute pulmonary embolism patients were obtained through the electronic medical record system (Goodwill E-Health Info Co., Ltd.). Imaging parameters on computed tomography pulmonary angiography (CTPA) images at the onset of the acute pulmonary embolism were measured and counted. Notably, we propose a new parameter based on CTPA images: the ratio of S-d (sum of residual segmental pulmonary artery diameter) to MPA(d) (the main pulmonary artery diameter) (S-d/MPA(d)). After 3 months of regular treatment for acute pulmonary embolism, patients were classified into a CPTE group or a non-CPTE group based on the presence of residual embolus. All data were compared between the CPTE group and non-CPTE group. Furthermore, logistic regression analysis was used to investigate risk factors for the progression of acute pulmonary embolism to CPTE. Results: A total of 77 cases (male:female = 1:1.26) were included in the study. There were 43 cases (55.84%) in the CPTE group and 34 cases in the non-CPTE group (44.16%). The results of univariate analysis showed that there were statistically significant differences between the 2 groups in risk stratification (chi(2)=8.043; P=0.005), protein S activity (chi(2)=5.551; P=0.018), the ratio of sum of residual segmental pulmonary artery diameter to the main pulmonary artery diameter (S-d/MPA(d); t2.103; P=0.039), Mastora score (U=362.500; P<0.001), and embolus location (chi(2)=16.969; P<0.001). However, there were no statistically significant differences between the 2 groups in treatment options (P=0.381). According to multivariate logistic-regression analysis, protein S activity <55% (P=0.025), Sd/MPA(d) >= 1.97 (P=0.011), and an embolus being located in the central pulmonary artery (P<0.001) were independent risk factors for chronic persistence of thromboembolism following acute pulmonary embolism. Conclusions: The protein S activity, location of the embolus, and S-d/MPA(d) on CTPA at the onset of acute pulmonary embolism may suggest the progression of acute pulmonary embolism to CPTE.