Honey has antimicrobial, antitumor, antioxidant, and anti-inflammatory effects. However, there have been few studies regarding the effects of manuka honey on bone metabolism and gut microflora. This study investigated the effects of manuka honey combined with α-cyclodextrin, Manuka Honey with Cyclopower TM (MHCP) on bone metabolism and caecal bacterial contents in ovariectomized (OVX) mice. Seven-week-old female Balb/c-strain mice were divided into four groups: sham-operated (sham) group, OVX group, and OVX mice that were fed a diet containing 5% or 10% (w/w) MHCP. After 9 weeks, the mice were sacrificed, and serum, uterus, caecum, and femur samples were obtained. Successful removal of the ovaries and induction of the osteoporotic process in OVX mice were demonstrated by a significant decrease in uterine weight and a significant increase in receptor activator of NF-κB ligand (RANKL) mRNA expression of the femur, compared to sham, respectively. Compared to the OVX group, MHCP reduced serum C-terminal telopeptide of type Ι collagen concentration as well as RANKL and nuclear factor of activated T-cells c1 (NFATc1) mRNA expression of the femur. Furthermore, MHCP increased caecal bifidobacteria and bacteroides contents. These results suggest that the MHCP expressed prebiotic effects, which might reduce bone resorption in OVX mice.