Object: In order to promote the functional recovery of median nerve rupture patients, this paper proposes an ultrasound-guided percutaneous nerve stimulation regimen based on finite element modeling. Method: First, according to anatomy feature, a multi-layer human forearm model is constructed. What’s more, taking current density and activate function as optimization indicators, the percutaneous nerve stimulation regimen is designed with finite element modeling, including electrical needle angel, distance and position. Finally, to test the performance of designed regimen, a total of 22 patients with median nerve rupture participate in the clinical randomized controlled trial. And the clinical treatment effect is evaluated with BMRC, grip strength, functional score of median nerve and DASH scores. Results: The designed percutaneous nerve stimulation regimen is that, parallel to each other, electrical needles are located at both ends of the injury nerve with a distance of 3 cm. Besides, clinical trial results show that, after treatment the difference in sensory function was statistically significant. In terms of motor function, the BMRC of motor and grip strength are improved in both groups after treatment and there are significant differences between groups. Besides the grip strength improvement of experimental group is 4 times higher than that of control group. On global function, the DASH scores are reduced by 29% with experimental group but only 8% with control group; functional score of median nerve improved by 24% in the experimental group and by 22% in the control group, but the difference between groups is statistically significant after treatment. Conclusion: Clinical trial results demonstrate that the designed percutaneous nerve stimulation regimen can significantly improve the sensory, motor and global function of median nerve rupture, which is a potential clinical treatment regimen. Trial registration: ChiCTR, ChiCTR2000030790. Registered14 march 2020, http://www.chictr.org.cn/ChiCTR2000030790