Background: This paper investigates the problems regarding caffeinated drinks intake, late chronotype, and increased body mass index (BMI) among medical students at a Chinese university. Methods: This cross-sectional study was conducted in 2018 with 616 medical students from Chongqing Medical University in Chongqing, China, whose information were collected by a self-reported questionnaire that included four sections: Demographic characteristics; Caffeinated drinks intake and physical state; Morningness-Eveningness Questionnaire; Depression Anxiety Stress Scale 21. Multiple mediation analyses were conducted to test the impact of late chronotype on increased BMI through caffeinated drinks consumption through two models. Results: The significantly mediated effect of caffeinated drinks consumption was revealed (estimate: −0.01, SE = 0.01, 95% CI [−0.02, −0.01]), and which played a positive role in linking late chronotype (B = −0.01, SE = 0.01, p < 0.001) and increased BMI (B = 1.37, SE = 0.21, p < 0.01), but their significant association did not be found in reversed model. In addition, physical activity and inactivity times demonstrated significant indirect effects in the two models. Conclusions: Interventions should focus on reducing caffeinated drinks intake and sedentary behavior time, enhancing physical activity among medical students.