Purpose To investigate the effects of emphysema, body composition, and blood biochemistry on bone mineral density (BMD) in a health checkup population with radiographic emphysema (RE). Methods RE subjects (n = 551) were divided into normal BMD (n = 204) and low BMD (n = 347) groups, and 551 1:1 age- and sex-matched non-RE subjects were enrolled. Differences in demographics, blood biochemical parameters, and body composition were compared between both two groups. Multivariate logistic regression was used to assess factors of low BMD in RE subjects. Result RE subjects had lower BMD, body mass index, fat area, albumin, and high-density lipoprotein cholesterol (HDL-C). Skeletal muscle area (SMA), blood pressure, and other biochemical indicators were higher in RE subjects than in non-RE subjects (all P < 0.05). In RE subjects, the low-BMD group was older, with lower hemoglobin, platelet count, albumin, and globulin, and had higher LAA% than the normal BMD group (all P < 0.001). Except for triglyceride, all lipid profiles were much higher in the low-BMD group (P < 0.05). Multivariate logistic regression showed that age > 62 (OR, 5.073 [95%CI: 3.366-7.645]; P < 0.001), percentage of low-attenuation areas (OR, 1.045 [95%CI: 1.014-1.077]; P = 0.004), and HDL-C (OR, 2.440 [95%CI: 1.246-4.779]; P = 0.009) were risk factors while SMA (OR, 0.995 [95%CI: 0.991-1.000]; P = 0.03) was a protective factor for low BMD in RE subjects. Conclusion In health checkup individuals with RE, RE extent, age, and HDL-C are independent risk factors for low BMD while SMA is a protective factor, suggesting that these should be considered when evaluating risk for low BMD.