The system thinking is a kind of new thinking mode that fostering the creative ability. It already has some successful applied experience abroad, particularly in education. In the chemistry teaching ——especially the calculation of chemical equation of high schools,students are always puzzled by the numerous and complicated superficies of chemical equation and hardly grasp its mathematics essence,which result in bad teaching effect. This dissertation makes some beneficial quests. Aiming at the relevant problem of the calculation of chemical equation, we put up some teaching practice in 5 classes by using the system thinking method and its related software STELLA, such as the teacher's brief introduction to the software, the basic calculation model establishment way and student’s activity etc. In this process, students can hold the calculation regulation more effectively. At the same time, the study moving ability between teachers and students also improves dramatically, which leads to the exciting development in other realms.