Targeted muscle reinnervation (TMR) can improve amputees’ movement ability by providing simultaneous and intuitive control of artificial limbs. However, little is known about whether TMR can relieve the phantom limb pain and how intramuscular nerve branches are distributed in the targeted muscle after the operation. The purpose of this study is to investigate the effects of TMR on phantom limb pain and to explore the possibility of post-operative neuranagenesis in rats. The rat model was established by sciatic nerves transaction (SNT group) and the proximal ends of these nerves were grafted into targeted muscles (TMR group). The degree of the phantom limb pain was measured by observing the autotomy behaviors of rats. The pilot results show that rats in the sham group have no autotomy behaviors, while rats in SNT group and TMR group show typical autotomy behaviors two days after the operations and the behaviors become worse gradually. However, the TMR group show obviously less pain than the SNT group. Meanwhile, some small new branches rising from the transferred nerves could be observed in targeted muscle with the aid of Sihler’s nerve staining technique. The experimental results suggest that TMR can possibly alleviate the phantom limb pain and the transferred nerve can regenerate to innervate with the targeted muscle.