Background: Chronic thromboembolic pulmonary hypertension (CTEPH), a major complication of acute pulmonary embolism (PE), carries significant morbidity and mortality. Early identification is critically important to prevent disease progression. Objective: We evaluated the associated risk factors of CTEPH in patients after acute PE. Methods: A prospective cohort study of consecutive patients with first episode of acute PE was conducted. Patients were followed for up to 5 years. Echocardiography was performed to screen pulmonary hypertension (PH). Suspect patients were further evaluated by right heart catheterization (RHC) and pulmonary angiography (PA). If invasive procedures were unacceptable, PH was diagnosed by a systolic pulmonary artery pressure (SPAP) greater than 50 mmHg by echocardiography at rest. Results: From 2006 to 2011, 614 patients with acute PE were included. Ten patients were diagnosed with CTEPH. The cumulative incidence of CTEPH after a first episode of acute PE was 1.7% (95% CI 0.7-2.7%) at three years, without subsequent increasing. History of varicose veins of lower limbs (HR 4.0, 95% CI 1.1-14.4, p=0.031), SPAP over 50mmHg at initial episode of acute PE (HR 28.7, 95% CI 3.2-254.0, p=0.003), intermediate-risk PE (HR 1.2, 95% CI 1.0-1.4, p=0.030), and the higher CT obstruction index at three months after acute PE (HR 1.1, 95% CI 1.0-1.2, p=0.001) were associated with increased risk of CTEPH. Conclusions: CTEPH is not a rare complication of acute PE in Asian population. Physicians should be aware of patients with history of varicose veins of lower limbs, high level of SPAP at acute PE, intermediate-risk PE and residual emboli in the follow-up period.