Abstract System thinking in chemistry (STC) emphasizes the relationships within the subsystems in chemistry, and the relationships between chemistry system and other subject systems, which is useful for learners to integrate and apply chemistry knowledge for the chemical phenomenon explaining and chemical issues solving. It is easy for students to get lost in the complicated conceptual system because of the interwoven internal and external systems, which means to represent STC and to clarify different systems’ interaction by employing Systems-Oriented Concept Map Extension (SOCME), Object-Process Methodology (OPM),Behavior Over Time Graphs (BOTG),Causal Loop Diagrams (CLD), Stock and Flow Diagrams (SFD), and other graphical tools. Based on the STC connotation, it can be used to cultivate chemistry learners’ STC and reform education practices by carrying out the teaching reform of “chemical equilibrium”, exploring green chemistry course construction, and conducting game-based learning, service learning, deep learning, project-based learning, workshops or seminars. The key to further develop STC teaching practice is the transverse correlations between chemistry system and other disciplinary systems, and the lengthways analytic relationships within chemical subsystems. Therefore, in order to carry out STC teaching practice and improve the development of students’ STC, chemistry practitioners need to work with other subject researchers and educators, to focus on the social application of chemical knowledge, to grasp the essence and characteristics of chemistry, and then to build up interlaced multi-system influence relation around chemical concepts and social issues.