Background Since being proposed half a century ago, problem-based learning (PBL) and team-based learning (TBL) have been two popular teaching approaches used in Chinese basic medical education. To compensate for the shortcomings of lecture-based learning (LBL), both PBL and TBL can greatly benefit students. This study compares the differences of PBL and TBL on active learning and final academic scores in Chinese basic medical curriculum at Shantou University Medical College (SUMC). Methods Ten Year 4 and thirteen Year 3 medical students, enrolled in 2015 and 2016 at SUMC, were selected for TBL and PBL, respectively. In the homeostasis module, a basic-medical curriculum used in China, TBL was used for Year 4 students at their 3rd year, and PBL was used for Year 3 students. Student feedback was collected through a questionnaire. Academic achievement was based on their final examination scores. Each grade used the same final examination paper, which included both memorization and clinical application questions, as students in the traditional LBL class. Quantitative data were analyzed by t- and nonparametric tests. Results All students completed the questionnaire. Most students (PBL:62%, TBL:90%) thought the teaching approach they used was good for training clinical thinking, but PBL required more time and imposed a greater study burden. However, PBL students received higher scores than LBL students for clinical application essays (p < 0.05), whereas there were no differences in memorization problem scores. Final academic scores showed no significant differences between TBL and LBL students (p > 0.05). Conclusion Despite the differences in the culture of learning between China and the West, TBL and PBL are two popular teaching approaches among Chinese medical students. In Chinese basic medical education, PBL is more effective in training clinical thinking, while in TBL, students spend less time with problems and are helped by the professors. The relevant assessment system and teacher training system should be perfected.