Objective: To explore the clinical phenotype distribution of chronic kidney disease-mineral and bone disorder (CKD-MBD) in maintenance hemodialysis (MHD) patients and its related influencing factors. Methods: A total of 1362 MHD patients were included, and their baseline data such as serum phosphorus, calcium, and intact parathyroid hormone (iPTH) were collected. K-means clustering analysis was used to classify the patients into two phenotypes. Univariate analysis was conducted on the general data and laboratory test results of the patients, and multivariate Logistic regression analysis was used to explore the independent factors related to different phenotypes. Results: Cluster analysis divided the patients into two groups. Phenotype 1 (n = 356) was the uncontrolled MBD type, characterized by serum phosphorus and iPTH levels significantly higher than the clinical control targets; phenotype 2 (n = 1006) was the relatively controlled MBD type, with all indicators within the target ranges. Serum calcium levels in both groups were within the range recommended by the Kidney Disease: Improving Global Outcomes guidelines. Multivariate Logistic regression analysis showed that age (OR = 1.032) and spKt/V (OR = 1.684) were negatively correlated with the uncontrolled MBD type, while serum uric acid (OR = 0.997), total cholesterol (OR = 0.817), and serum potassium (OR = 0.679) were positively correlated with the uncontrolled MBD type (all P < 0.05). Conclusion: There exists an uncontrolled phenotype in MHD patients characterized by normal serum calcium, high serum phosphorus, and high iPTH, which is independently related to age, dialysis adequacy, and some metabolic indicators. Individualized management should be strengthened for high-risk patients.