Objective Verification of designed cognitive ability model of medical comprehensive written examination for National Medical Licensing Examination in rural general practitioners by sample data and to provide suggestion on future improvement. Methods Confirmatory factor analysis is applied to test the fitness and to improve the designed cognitive model for various subject contents. Results The designed model is improved by altering western medicine understanding to application and traditional Chinese medicine application to understanding. Fitness indexes are above standard level (>0.95). Conclusions Most part of the designed model is supported by candidate data (>80%). High correlation between latent variables could explain the alternation of the model. The improved model is both scientific and reasonable. Suggestions are provided to better define the cognitive levels and to enhance SME training.