Background Clinical Practice Guidelines (CPGs) play an important role in clinical practice, and they require appropriate evaluation, especially in application. This study explores the application evaluation method of CPGs for Traditional Chinese Medicines (TCM). It uses the Analytic Hierarchy Process (AHP) and clinical cases to evaluate the consistency between CPGs of TCM and clinical practice. Methods To evaluate the consistency between CPGs of TCM and clinical cases, a 3-level AHP construction was built. Weightings were calculated by collecting questionnaires according to AHP theory. To test the evaluation system, a retrospective study was performed. The study evaluated the China Association of Chinese Medicine's Guidelines for Diagnosis and Treatment of Common Internal Diseases in Chinese Medicine Diseases of Modern Medicine (CPGs of DTCID) (ZYYXH/T50-135-2008). A total of 150 cases were involved. The evaluation system was used to assess the consistency between CPGs of DTCID and clinical cases of angina pectoris. Results The results showed that the overall consistency between CPGs of DTCID and the 150 cases was 42.32 +/- 6.94%, ranging from 35.21 to 63.37%. The overall consistency was not affected by age, gender, type of angina pectoris, condition of percutaneous coronary intervention (PCI), or angina classification as determined by the Canadian Cardiovascular Society. The consistencies of each index were as follows: Diagnosis of TCM, 100%; Diagnosis of Western medicine, 100%; Syndrome classification, 38.25 +/- 4.40%; Syndrome key point, 34.17 +/- 8.15%; TCM Decoction, 31.08 +/- 23.64%; TCM particular treatment, 7.92 +/- 19.13%; and Recuperation and prevention, 0. The most frequent syndromes were qi-deficiency, phlegm and blood stasis (n = 124) (82.7%). The overall consistency of qi-deficiency, turbid phlegm and blood stasis was lower than the overall consistency of the group without that syndrome. The difference was statistically significant (P < 0.05). 42 cases (28%) applied the TCM decoction recommended by CPGs of DTCID. Of these, Gualouxiebaibanxia decoction was applied in 34 cases. Wendan decoction, the most frequently used, was applied in 64 cases (42.7%). Conclusion This study indicates that the AHP system can perform quantitative evaluation of consistency between TCM CPG and clinical practice. It also found the factors affecting the application of TCM CPGs and might indicate the need for revisions of CPGs.