Estrogen deficiency is the main factor underlying postmenopausal osteoporosis. A large number of neuropeptides, which regulate skeletal metabolism, potentially represent a regulatory pathway for the pathogenesis of osteoporosis. The aim of this study was to explore factors involved in the regulation of bone-related neuropeptides and their association with estrogen deficiency and bone metabolism. Thirty adult female Sprague-Dawley (SD) rats were randomly divided into a control group with sham surgery (n = 15) and an ovariectomy group with bilateral oophorectomy (n = 15). After 16 weeks, serum estrogen was reduced,CTX-1 was increased and P1NP was not significantly affected in the ovariectomy group and a model of osteoporosis was established. We then investigate the gene expression and protein levels of a range of neuropeptides and their receptors, including substance P (SP) and tachykinin receptor 1 (TACR1), calcitonin gene-related peptide (CGRP) and calcitonin receptor-like (CALCRL), vasoactive intestinal polypeptide (VIP) and receptor 1 and 2 (VPAC1, 2), neuropeptide Y (NPY) and receptor Y1 and Y2, in the brain and femora. Ovariectomy reduced TACR1, CGRP, CALCRL, NPY, NPY Y2 in the brain, but increased TACR1 and decreased SP, CALCRL, VIP, VPAC2 in the bone. Collectively, our data revealed that the pathogenesis of postmenopausal osteoporosis is associated with the regulation of SP, CGRP, VIP, and NPY. These novel results are of significant importance in the development of neuropeptides as therapeutic targets.