Background: Critical thinking (CT) is an essential competency for medical students. This study’s aim was to evaluate Chinese medical students’ disposition for CT and to explore the impact of current trends in medical education on students’ CT development. Methods: We used multistage stratified cluster sampling to recruit a total of 1241 medical students among five different years of training and from three medical institutions in China. The Critical Thinking Disposition Inventory-Chinese Version (CTDI-CV) and self-reported information were used to collect cross-sectional data. Based on the data from the CTDI-CV, 112 medical students in clinical course training from a single institution continued one-year follow-up. Their one-year CTDI-CV score changes were collected regarding various medical education variables. Results: The mean CTDI-CV score of the 1241 medical students was 287.04 with 729 (58.7%) students receiving a score of 280 or higher. There were statistically significant differences in schools attended(F = 3.84, P < 0.05), year of school attended(F = 10.32, P < 0.001), GPA(F = 6.32, P < 0.01), weekly time spent learning after class(F = 14.14, P < 0.001), attitude toward medicine(F = 28.93, P < 0.001), desire to be a doctor after graduation(t = − 3.35, P < 0.001), familiarity with CT(F = 20.40, P < 0.001), and perception of importance of CT(F = 22.25, P < 0.001). The participants scored the highest on the CTDI-CV subscales of “inquisitiveness” and the lowest on “truth seeking.” The 112 students in the longitudinal study had significantly lower total CT scores after one academic year follow-up. Conclusions: Chinese medical students generally exhibited positive CT dispositions. The cross-sectional survey and one-year longitudinal study indicated that students’ CT disposition diminished as they progressed through traditional medical training. Our study contributes to understanding the status of Chinese medical education of and influential factors on medical students’ CT disposition.