Background and Aims Lower extremity deep vein thrombosis (DVT) is a common complication in hospitalized patients. The current approach to its treatment focuses on rapid thrombus removal to reduce the occurrence of post-thrombotic syndrome. The main methods include catheter-directed thrombolysis (CDT) and mechanical thrombus removal (PMT). However, there is still some controversy regarding the indications for CDT and PMT, and there needs more relevant research in health economics, making it difficult to assess the benefits of CDT and PMT treatments for patients. This study aims to comprehensively evaluate and compare the benefits of CDT and AngioJet treatments in patients with lower extremity DVT who underwent surgical treatment in order to provide recommendations for clinical doctors in selecting appropriate treatment methods and maximize the benefits for patients in terms of efficacy, quality of life, and economics.Methods Clinical and follow-up data were collected from patients diagnosed with lower extremity DVT and treated with CDT or AngioJet in the Department of Vascular Surgery from December 2018 to August 2020. The analysis included efficacy (syndrome scores), cost-effectiveness, follow-up color Doppler ultrasound results, Villalta scores, and CIVIQ-2 scores.Results A total of 79 patients with lower extremity DVT were included, with 47 patients treated with AngioJet (AngioJet group) and 32 patients treated with CDT (CDT group). There were no significant differences in general characteristics and consumable usage between the two groups of patients (all P>0.05). Symptoms significantly improved in both groups after treatment, with a higher recovery rate in the AngioJet group compared to the CDT group (34.04% vs. 12.50%, P<0.05). There was no significant difference in the length of hospital stay between the two groups (P>0.05). The treatment cost was significantly higher in the AngioJet group compared to the CDT group (77 498.11 CNY vs. 66 092.58 CNY, P<0.05). However, the cost per 1% recovery rate was lower in the AngioJet group compared to the CDT group (2 579.83 CNY vs. 5 287.41 CNY). There was no statistically significant difference in the postoperative follow-up color Doppler ultrasound scores between the two groups (P>0.05), but both the Villalta scores and CIVIQ-2 scores indicated that the treatment efficacy in the AngioJet group was superior to that in the CDT group (both P<0.01).Conclusion AngioJet and CDT are effective in treating lower extremity DVT, but AngioJet is a more cost-effective treatment option for patients with lower extremity DVT while providing better quality of life. In economically feasible situations, the AngioJet treatment option may be considered.