Objective　To explore specific practice of the trinity of ‘structure-property-appli-cation’ in pharmaceutical chemistry teaching and to evaluate the teaching effect. Methods　Students of 2009 grade three-year pharmacy class 1 in Luohe Medical College（n=62） were selected as control group and the 2010 grade three-year pharmacy class 1（n=70） as experimental group. Students in experimental group were taught by the trinity of ‘structure-property-application’ teaching while those in control group by traditional teaching method. Quantitative research and qualitative research was combined. Comparison of comprehensive test results was used in quantitative research and question-naire for students in experiment group was used in qualitative research to observe the teaching pro-cess. Qualitative and quantitative research data were statistically analyzed by SPSS 16.0 software and the comprehensive test scores were analyzed by rank sum test. Result　Comprehensive test scores were significantly improved in experimental group than in control group， with statistical differences（Z=2.880， P=0.04）. Results of questionnaire showed that 90.00%（63/70） or more students in experiment group supported trinity teaching methods and the effect was satisfactory. Conclusions　Implementa-tion of the trinity teaching methods can greatly improve students' enthusiasm and initiative and en-hance students' innovative ability and problem-solving ability. It can also improve the teaching quality of pharmaceutical chemistry.