Abstract According to the characteristics of structural chemistry and students' confusion in learning, this paper explored the small thematic teaching method of structural chemistry, and discussed the teaching situation from the aspects of teaching difficulties, basic conception, small thematic design and implementation, etc. Moreover, this paper proposed 24 new themes with guiding analysis. The results indicated that the small thematic teaching method was feasible and adjustable, which could effectively stimulate students' leaning initiative and cultivate students' comprehensive quality and ability.