Early catheter-directed thrombolysis (CDT) for lower extremity deep vein thrombosis (LEDVT) can reduce post-thrombotic morbidity and the AngioJet thrombectomy is a new therapy that can be selected for the treatment of LEDVT. We performed a systematic review and meta-analysis of clinical trials comparing AngioJet versus CDT to assess the efficacy and safety of AngioJet thrombectomy. We systematically searched PubMed and Embase for clinical trials that published before November 1, 2020 and compared AngioJet thrombectomy and CDT in the treatment of LEDVT. We meta-analyzed effective rate of treatment, serious complications, PTS, Villalta score, duration of treatment and drug dose. AngioJet does not result in a significant difference in the effective rate (OR 1.00, CI 0.73-1.36, P = 0.98; I2 = 0%) and complications (OR 1.16 CI 0.84-1.61, P = 0.36; I2 = 39%) compare to CDT. And there was a statistically significant decrease in incidence of PTS (OR 0.58 CI 0.37-0.91, P = 0.02; I2 = 0%) and Villalta score (OR −1.86 CI −3.49 to −0.24, P = 0.02; I2 = 34%) for AngioJet compared to CDT. In addition, there was a statistically significant decrease in duration of the treatment (OR −2.45 CI −2.75 to −2.15, P < 0.0001; I2 = 95%) and drug dose (OR −3.15 CI −3.38 to −2.93, P < 0.0001; I2 = 98%) between AngioJet and CDT. AngioJet results in a low severity of PTS compared to CDT therapy. Moreover, the average duration of treatment and thrombolysis time was shorter in the AngioJet group compared to the CDT group. However, the AngioJet group was not significantly different in effective rate of treatment and serious complications compared to the CDT group.