Acute lower extremity deep venous thrombosis (LEDVT) is a common vascular emergency with significant morbidity risks, including post-thrombotic syndrome (PTS) and pulmonary embolism. Traditional treatments like catheter-directed thrombolysis (CDT) often result in variable success rates and complications. To investigate the therapeutic efficacy of percutaneous mechanical thrombus removal in acute LEDVT. A retrospective analysis was performed to examine 58 hospitalised patients with acute LEDVT between August 2019 and August 2022. The patients were categorised into the percutaneous mechanical thrombectomy (PMT) group (n = 24) and CDT group (n = 32). The follow-up, safety and treatment outcomes were compared between the two groups. The main observational indexes were venous patency score, thrombus removal effect, complications, hospitalisation duration and PTS. The venous patency score was 9.04 ± 1.40 in the PMT group and 8.81 ± 1.60 in the CDT group, and the thrombus clearance rate was 100% in both groups. The complication rate was 8.33% in the PMT group and 34.84% in the CDT group, and the difference was statistically significant (P < 0.05). The average hospitalisation duration was 6.54 ± 2.48 days in the PMT group and 8.14 ± 3.56 days in the CDT group. The incidence of PTS was lower in the PMT group than in the CDT group; however, the difference was not statistically significant (P < 0.05). Compared with CDT, treatment of LEDVT via PMT was associated with a better thrombus clearance rate, clinical therapeutic effect and PTS prevention function, but the difference was not statistically significant. Moreover, PMT was associated with a reduced urokinase dosage, shortened hospitalisation duration and reduced incidence of complications, such as infections and small haemorrhages. These results indicate that PMT has substantial beneficial effects in the treatment of LEDVT.