Postmenopausal women face increased risks of osteoporosis and cardiovascular diseases due to estrogen decline. This study investigated the effects of moderate-intensity continuous training (MICT) and high-intensity interval training (HIIT) on bone microstructure and cardiovascular risk factors in ovariectomized (OVX) mice. Results showed that both exercise regimens improved blood lipid profiles and vascular structure, reducing systolic blood pressure (−11.81% and −10.89%) and undercarboxylated osteocalcin (ucOCN) levels (−52.14% and −52.05%). However, moderate-intensity exercise was more effective in enhancing bone mineral density (+82.38% and +45.02%) and microstructure recovery. No significant correlation was found between ucOCN and cardiovascular disease risk factors, such as lipid parameters, systolic blood pressure, and vascular wall thickness. This study suggests that both exercise intensities can mitigate cardiovascular risks in OVX mice, which is independent of OCN. MICT is superior for promoting osteoporosis recovery.