Objective To investigate the short-term result of catheter directed thrombolysis (CDT) in treatment of acute deep venous thrombosis (DVT) in lower extremity. Methods A total of 289 cases of acute DVT in lower extremity who got treatment in Nanjing Drum Tower Hospital Group Suqian City People’s Hospital and Xuzhou Central Hospital from March 2013 to December 2014 were enrolled prospectively, and of them, 125 cases of system thrombolysis (ST) group underwent ST, 164 cases of CDT group underwent inferior vena cava filter placement (IVCF)+CDT. Clinical effect was compared between the 2 groups. Results Clinical symptoms of all cases were obviously relieved, and limb swelling was significantly reduced. Of the CDT group, 73 cases presented iliac vein compression syndrome (IVCS), and 43 cases of them underwent the percutaneous transluminal angioplasty and stent implantation. In CDT group, there was 1 case complicated by catheter displacement, 10 cases suffered from puncture site ecchymosis, 3 cases suffered from hematuria. In ST group, there was 1 case suffered from pulmonary embolism (PE), 14 cases suffered from bleeding gums, 22 cases suffered from hematuria, 3 cases suffered from skin and mucosa petechia, and 2 cases suffered from melena (didn’t need transfusion). The morbidity of ST group was higher than that of CDT group (P=0.002). There were 18 cases suffered from recurrence in ST group, 15 cases suffered from recurrence in CDT group, but there was no significant difference in the recurrence rate between the 2 groups (P=0.786). In addition, the dosage of urokinase, thrombolysis time, blood vessel patency score, thigh circumference after treatment, and calf circumference after treatment in ST group were all higher than those of CDT group (P<0.050), but the Villalta score in ST group was lower than that of CDT group (P<0.001). There was no significant difference in hospital stay (P=0.383). Conclusion For acute DVT in lower extremity, CDT has a superior short-term outcome with safety and feasibility.