SIRT3 has been speculated to affect osteoclast activity through its important roles in regulating mitochondrial function. It remains unclear whether SIRT3 affects osteoclast activity in female mice which is relevant to postmenopausal osteoporosis. We hypothesized that deletion of SIRT3 could modulate bone remodeling in female mice under physiological aging process or ovariectomy (OVX)-induced bone loss. We found that SIRT3 level was markedly increased in primary bone marrow-derived macrophages (BMMs) from both 26-month-old aged mice and OVX mice. Knockdown of SIRT3 in vitro inhibited osteoclast differentiation and mitochondrial biogenesis, and deletion of SIRT3 increased trabecular bone mass in female mice due to impaired osteoclastogenesis. The effect of SIRT3 on bone remodeling appears to be age-dependent as revealed by comparing the effect of SIRT3 deletion on 5-week-old, 3-month-old and 6-month-old female mice. Interestingly, Sirt3−/− mice were more resistant to bone loss following estrogen deficiency resulting from OVX. Our findings demonstrated that SIRT3 could play critical roles in bone remodeling and estrogen deficiency-induced bone loss in female mice, suggesting that SIRT3 and its downstream effectors might be potential novel therapeutic targets for the management of postmenopausal osteoporosis.