To cultivate computational thinking in medical students and meet their professional needs, this study reformed the programming course at Tianjin Medical University by introducing MATLAB programming. Different teaching strategies were adopted for undergraduates and postgraduates. For undergraduates, specialized application modules were designed according to their disciplinary characteristics, while for postgraduates, artificial intelligence medical application cases were incorporated. Additionally, an asynchronous Small Private Online Course (SPOC) was developed on the MOOC platform to provide students with a continuous computational thinking training environment. The results showed that post-reform satisfaction scores for the 2021 undergraduate cohort (98.27) and the 2023 postgraduate cohort (96.86) were significantly higher than those of the pre-reform 2020 undergraduate cohort (85.93) and 2022 postgraduate cohort (89.43). Students reported that the experimental content of the programming course was well-structured and effectively integrated with theory, enabling them to create impressive projects during programming practice. The MATLAB programming course successfully addressed the professional needs of medical students and enhanced their computational thinking skills, offering valuable insights for the development of programming courses in medical universities across China.