Objective: To evaluate long term effects of thrombolysis on patients with submassive pulmonary embolism (PE) through a prospective observational study.Methods: Total of 136 patients with acute submassive PE were recruited from January 2005 to October 2011.The patients were divided into two groups.The thrombolysis group (TT) received recombinant tissue plasminogen activator (TT group, n=79).The anticoagulant group (AT) received low molecular weight heparin (AT group, n=57).Echocardiography was performed at admission, 24 hours, 6 months, and 1 year.CTPA together with lung perfusion scan were performed on admission, at 7 days, 6 months, and 1 year.Results: The baseline characteristics and risk factors did not differ between TT group and AT group.Respiratory rate, Heart rate, and Systolic Blood Pressure improved within 2 hours in two groups.Systolic Pulmonary Arterial Pressure and Tricuspid Regurgitation improved to a greater extent in the TT group at 24 hours, and one year (P<0.001).Clot burden decreased more after thrombolysis, as compared to anticoagulation group at one week, and one-year follow-up (P<0.001).There was no lethal event due to bleeding in both groups.Recurrent PE were similar in both groups (2.5 % in TT vs.1.8% in AT).The rates of minor hemorrhages were 6.3% in TT group and 1.8% in AT group (P<0.05).Conclusion: Thrombolysis can led to greater improvement of right ventricular dysfunction compared to anticoagulation group and significantly reduced the clot burden of the submassive PE patients.