Objective To investigate the influence of metabolic risk factors on serum markers of bone metabolism and their relationship. Methods The data of patients with metabolic and bariatric surgery including blood glucose, triglyceride (TG), high density lipoprotein (HDL), bone specific alkaline phosphatase (B-ALP) and carboxy terminal peptide of type I collagen (CTX) were collected from department of gastrointestinal surgery in our hospital from January 2015 to April 2020. The patients were divided into two groups according to the median of B-ALP (≤14.24 μg/L, >14.24 μg/L) and CTX (≤0.36 μg/L, >0.36 μg/L). The clinical data and metabolic risk factors were compared between two groups and the clinical and metabolic factors correlated with parameters including B-ALP and CTX were analyzed. Results A total of 205 patients were included in this study with 81 males and 124 females There were significant differences in the parameters including systolic blood pressure, diastolic blood pressure, TG, HDL and the cases with lower HDL between B-ALP≤14.24 μg/L group and B-ALP>14.24 μg/L group (P<0.05). Between CTX ≤0.36 μg/L group and CTX >0.36 μg/L group, there were significant differences in gender, subcutaneous fat area and fasting blood glucose (P<0.05). B-ALP correlated with age and HDL negatively, and with systolic blood pressure, diastolic blood pressure and TG positively. CTX correlated with age and fasting blood glucose negatively. Logistic regression analysis showed that the risk of abnormal B-ALP increased significantly in patients with higher HDL (OR=2.931, 95% CI:1.585-5.421, P=0.001). Patients with larger area of subcutaneous fat decreased risk of abnormal CTX significantly (OR=0.381, 95% CI:0.194-0.748, P=0.005), while those with higher HDL had higher risk of abnormal CTX significantly (OR=2.067, 95% CI:1.118-3.824, P=0.021). Conclusions It was shown that lower HDL, higher fasting hyperglycemia and hypertension have influence on bone metabolism indexes of patients with metabolic and bariatric surgery.