Most recent studies attribute residual limb pain to peripheral pathological changes of the stump. However, in this paper, we focus on its associations with the residual limb length, usage, as well as the metabolic and functional alterations of the brain. The secondary somatosensory cortex (S2), one important area involved in pain intensity discrimination, was selected as the region of interest. Twenty-two upper-limb amputees were recruited and divided into two groups, i.e., amputees with residual limb pain (9/22) and without residual limb pain (13/22). The residual limb length, usage, as well as the metabolite concentration, resting-state activity and BOLD responses to the tactile stimulation in the contralateral S2, were compared between the two groups and correlated with the pain intensity. The amputees with residual limb pain showed significantly shorter length and less usage of the residual limb than the amputees without residual limb pain, and the pain intensity was significantly negatively correlated with the residual limb length and usage. In addition, the pain intensity was significantly correlated with the tNAA/tCr ratio, resting-state fALFF in the slow-4 band, and BOLD response to the tactile stimulation in the contralateral S2, although there were no significant group differences. Regression analysis suggested that residual limb pain is associated with shorter residual limb length and less residual limb usage.