Objective To evaluate the long-term effects of thrombolysis on patients with submassive pulmonary embolism (PE). Methods Data of 136 patients with acute submassive PE and low risk of bleeding were prospectively collected from January 2005 to October 2011 in a single medical center. Patients received recombinant tissue plasminogen activator (r-tPA) plus low molecular weight heparin (LMWH, TT group, n = 79) or LMWH alone (AT group, n = 57), depending on treating physician's recommendation and patient's preference. Echocardiography was performed at admission, 24 h, 6 and 12 months to evaluate right ventricular function. Computed tomography pulmonary angiography (CTPA) and lung perfusion scan were performed on admission, at 7 days, 6 and 12 months to evaluate clot burden. Results Seventy-nine patients received r-tPA plus LMWH (TT group) while 57 received LMWH alone (AT group). The baseline characteristics and risk factors did not differ between the two groups. Respiratory rate, heart rate, and systolic blood pressure improved within two hours in both groups. Systolic pulmonary arterial pressure and tricuspid regurgitation improved to a greater extent in the TT group at 24 h, and at 12 months (P < 0.001), as compared to those in the AT group. At one week, and 12 months, clot burden decreased more in AT group, as compared to that in AT group (P < 0.001). There was no death 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 In submassive PE patient who has low risk of bleeding, thrombolysis plus anticoagulation can lead to greater improvement of right ventricular dysfunction and clot burden reduction as compared to anticoagulation therapy alone.