Background <p>Medical students face elevated health risks due to academic stress and a sedentary lifestyle. Given the geographical and ethnic diversity of Southwest China, it is particularly important to understand the factors associated with physical fitness and bone health in this population. However, evidence regarding the physical fitness and bone health of medical students in this region remains limited.</p> Methods <p>This cross-sectional study included 334 medical students (99 males and 235 females; aged 17–24 years) from Southwest China, comprising both Han and ethnic minority students. Body mass index (BMI) was calculated, a composite physical fitness index (PFI) was derived from six standardized fitness tests, and calcaneal bone mineral density (BMD) was assessed using quantitative ultrasound. Gender-stratified analyses, partial correlations adjusted for age and BMI, and multiple regression models were performed.</p> Results <p>Male students showed higher prevalences of overweight/obesity (18.18% vs. 5.96%) and osteopenia (6.06% vs. 2.98%) than females. A nonlinear association was observed between BMI and physical fitness, with normal-weight students demonstrating the highest PFI. No significant differences were observed between Han and ethnic minority students in physical fitness or bone health indicators. Muscle strength emerged as the strongest predictor of BMD, with bent-leg sit-ups predicting BMD in females (<i>B</i> = 0.290, <i>p</i> = 0.020) and pull-ups predicting BMD in males (<i>B</i> = 0.543, <i>p</i> = 0.014).</p> Conclusions <p>Physical fitness and bone health differed according to sex and BMI status among medical students in Southwest China. Muscle strength was identified as the most important modifiable factor associated with BMD. These findings support the development of sex-specific and culturally appropriate health promotion strategies to improve musculoskeletal health among ethnically diverse university populations.</p>