This study aimed to determine the association between the absolute mass, distribution, and relative ratio of body fat and muscle with the metabolically unhealthy (MU) phenotypes in normal weight and overweight/obesity in Yi people in China. The cross-sectional data from the Yi Migrants Study was used, which included 3,053 Yi people aged 20-80 years from the rural and urban sets. Participants were classified according to body mass index and metabolic status. Body composition including body fat percentage (BFP), fat mass index (FMI), visceral fat grade (VFG), muscle mass index (MMI), and muscle/fat ratio (M/F) were measured by bioelectrical impedance analysis. Restricted cubic spline and logistics regression models were used to test the associations between body composition parameters with MU phenotypes. Receiver-operating characteristic curves (ROC) were used to analyze the predictive value of MU phenotypes. Among the normal weight and overweight/obesity, 26.31% (497/1,889) and 52.15% (607/1,164) were metabolically unhealthy. Stratified by BMI, covariance analysis showed higher body fat (BFP, FMI, and VFG) and MMI in MU participants than in healthy participants. BFP, FMI, VFG, and MMI were positively associated with MU phenotypes both in normal weight and overweight/obesity after adjustment. M/F was significantly lower than MU participants and was negatively associated with MU phenotypes. BFP, FMI, VFG, and M/F could better predict MU phenotypes than BMI. We concluded that BFP, FMI, and VFG were positively associated with MU phenotypes, while M/F was negatively associated with MU phenotypes across the BMI categories in Yi people. Body fat and muscle measurement could be a valuable approach for obesity management.