Objective To investigate critical thinking disposition inventory on medical students to offer evidence for building a medical education model with core competency as guide, evidence-based medicine as carrier and lifelong learning as purpose. Methods Chinese Version of Critical Thinking Disposition Inventory was used to investigate the current status of critical thinking of 617 medical undergraduates and graduates of Sichuan University. Results The average total score was more than 280 points. Average total scores of medical students in different educational systems from high to low were 309 points (eight-year-program), 298 points (postgraduates), 287 points (seven-year-program) and 286 points (five-year-program), respectively. The scores of three items including “seek truth”, “systematicity” and “confidence” were lower than 40 points in students both of five-year-program and seven-year program. There was no significant difference in total scores and each item between genders and varied ages. Conclusion The main factors which influence critical thinking in medical students of China include education idea, teaching atmosphere, teaching methods and teaching evaluation system.