Basic medical laboratory courses (BMLCs) play an important role in medical educational courses helping the student acquire three important skills of surgical operating, collaborative learning, and problem solving. The outcome-based student assessment (OBSA) is a learning evaluation method that establishes specific evaluation points based on performance of students in three aspects: surgical operating, collaborative learning, and problem solving in the BMLC curriculum practices. The purpose of the present randomized controlled trial study is to explore the efficiency of OBSA program in BMLCs. The 233 students attending BMLCs were randomly divided into 2 groups, 118 in the OBSA group and 115 in the control group. We conducted multiple-choice examination questions (MCQs) test and two questionnaires with the method of two-sample t test for statistics. The results of MCQs in total eight BMLC blocks showed that the academic performance of the OBSA group was significantly better than that of the control group (P < 0.05). In addition, the average scores of direct observation of procedural skills (DOPS) and mini-experimental evaluation exercise in OBSA group were significantly higher than those in control group (P < 0.05). The majority of the medical students preferred the OBSA and considered OBSA could effectively improve their surgical operating skills (83.9%), collaborative learning skills (92.1%), and problem-solving skills (91.1%). From the above, OBSA is an effective evaluation method for the implementation of the BMLC curriculum.