Objectives: Loss of bone mass may affect the progression of atherosclerosis. We investigated the relationship between low bone mineral density (BMD) and subclinical atherosclerosis in rural China. Methods: In total, 333 men and 421 postmenopausal women aged 55–65 years were enrolled. BMD was measured in the lumbar spine, femoral neck, and total hip using dual-energy X-ray absorptiometry. Subclinical atherosclerosis was defined as increased carotid artery intima-media thickness (CIMT ≥0.9 mm), the presence of carotid plaques, high brachial-ankle pulse wave velocity (baPWV ≥1,400 cm/s), and low ankle-brachial index (ABI ≤1). Binary logistic regression analyses were used to estimate the association between low BMD and subclinical atherosclerosis. Results: There was no significant difference in BMD between the normal group and the subclinical atherosclerosis group. After full adjustment for the relevant covariates, a boundary significant association was found between low BMD in the femoral neck and baPWV in postmenopausal women (odds ratio = 1.77, p = 0.049). After full adjustment, neither BMD nor low BMD were significantly associated with subclinical atherosclerosis in men or postmenopausal women. Conclusions: Low BMD is not associated with subclinical atherosclerosis in Chinese individuals aged 55–65 years resident in rural China.