Objective This paper analyzes equating methods applied in Standardized Competence Test for undergraduates of clinical medicine based on classical test theory (CTT) and item response theory (IRT) in order to explore a more suitable equating method. Methods The research uses four equating methods based on the CTT and six equating methods based on the IRT.CTT equating methods include Tucker observation score linear equating method,Levine observation score linear equating method, equipercentile equating smoothing method and equating standard error equating unsmoothed method. While in the one-parameter model and two-parameter model of IRT, three calibration methods are used which are linking separate calibration, concurrent calibration and fixed Item Parameter Calibration. The stability of the 10 equating results is analyzed by the equating standard error. Results The results show that the equating standard error of CTT method is 0.7~1.6, while the equating standard error of IRT method is 0.2~0.6, IRT equating standard error is smaller than CTT equating method. Among four CTT equating methods, the equating standard error of Tucker observation score linear equating method is 0.7 as the smallest one, the error of equipercentile equating method is 1.6 as the largest one. Among six IRT equating methods, the result of one-parameter model is better than that of two-parameter model and the error of fixed item parameter calibration is the smallest one in one-parameter model, which the equating standard error is 0.2. Conclusions The fixed item parameter calibration in one-parameter model of IRT can be selected as the equating method of this test. Through equating, the score of year 2 is improved, and the eligibility criteria remain unchanged, which effectively achieves the score comparability and ensures the fairness of the test.