Objective To investigate the amputation-related pain and quality of life (QoL) between the amputees with transfemoral amputation (TFA) and transtibial amputation (TTA) 10 years after the Wenchuan earthquake, and compare the effects of two different amputation level on the long-term functional rehabilitation of amputees. Methods A total of 305 amputees from Center of Comprehensive Service of Disabled of Deyang for the disabled 10 years after the Wenchuan earthquake were selected for cross-sectional study from February to June 2018. Through face-to-face interview, the basic information of amputees was collected and the evaluation of Prosthetic Evaluation Questionnaire (PEQ) was completed. The amputees were divided into TFA group and TTA group according to the amputation level. Results A total of 53 amputees were included, including 27 in the TFA group and 26 in the TTA group. The PEQ scores showed that the prevalences of phantom limb sensation (96.3% vs. 65.4%; χ2=6.372, P=0.012) and phantom limb pain (92.6% vs. 69.2%; P=0.039) in the TFA group were significantly higher than those in the TTA group. There was no significant difference with regard to the intensity of amputation-related pain between the victims with TFA and TTA (P>0.05). However, the TFA group were more bothered by phantom limb sensation than the TTA group (52.9±24.1 vs. 35.9±26.7; t=2.108, P=0.042), there was no significant difference in other indexes (P>0.05). There was no significant difference in QoL between the TFA and TTA groups (P>0.05). Conclusions The phantom limb sensation, phantom limb pain, residual limb pain, non-amputated limb pain and back pain are still prevalent among the victims with TFA and TTA 10 years after the Wenchuan earthquake. The higher amputation level is associated with increased prevalence of phantom limb sensation and phantom limb pain, as well as more bothersomeness of phantom limb sensation. The amputation level appeares to have no impact on the long-term QoL.