OBJECTIVE：To improve the teaching quality of Natural Medicine Foundation and help students better grasp the basic skills of distinguishing common natural medicines. METHODS： Comparison method was used to integrate teaching contents and organize classroom teaching， and the effectiveness of teaching was evaluated. RESULTS： The traditional teaching material system was broke to integrate comparable content together by comparing the common and difference to integrate the content of the comparability， comparison of differences in similarities included the comparison of herbal medicinal parts of similar finishing， the comparison of Chinese medicinal herbs with the same typical characters； comparison of differences in similarities included the comparison of similar overall properties of the herbs， characters of traditional Chinese medicinal materials from different sources， drug name medicine approximation comparison， precious medicinal herbs genuine and counterfeit goods traits. Infiltration comparison method was used in different types of courses and the teaching of different teaching links to guide students to learn to use the comparative thinking to obtain knowledge. CONCLUSIONS：According to the application of comparative method in the teoching of Natural Medicine Foundation， students have improved the performance and learning ability. It is suggested to apply the comparative method moderately and timely and insist in student-centered，in addition，comparative method shoud be researched and applied with development view.