This analysis is to observe and explore the effect of learning objective on medical education based on cognitive neuroscience, and to provide the basis for improving learning objective of medical education students. In this analysis, 200 medical education students in Southwest Medical University are sampled by stratified cluster sampling method. Questionnaires are used to conduct field investigation of the basic situation, learning objective and learning motivation. 100 students are in the experimental group and 100 students are in the control group. The students in the experimental group are taught with cognitive neuroscience while the students in the control group are taught in the conventional teaching model. Learning objective of students in the two groups is compared. By applying cognitive neuroscience to medical education, students have a strong learning objective. In the post-test, learning objective of students in the experimental group obviously increases from 78.3562 to 87.395 while there is no significant change (only from 77.7935 to 78.0284) in the control group. The standard deviation of the experimental group decreases from 11.2078 to 7.5392, and the minimum value increases from 57.00 to 69.00, indicating that learning objective gap of students in the experimental group has been narrowed and the polarization has got improved. The result of classification Logistic regression shows that the application of cognitive neuroscience to medical education can effectively improve students’ learning objective. The learning of medical education based on cognitive neuroscience is strong, which can be guided and improved by creating a learning atmosphere, strict teaching management and professional ideological education strategies.