The implementation of systems approaches and systems thinking has been considered as an important parameter for reforming chemistry education and practice. The “Systemic Approach to Teaching and Learning (SATL)” strategy is a teaching-learning approach which is based on the development and use of cyclic concept mapping procedures, known as systemics, for teaching as well as for students’ assessment, known as SAQs. The SATL strategy focuses on the enhancement of students’ systems thinking skills, which are believed to enhance their understanding of relevant science concepts. The aims of this study were: (a) To investigate the effect of the implementation of the SATL strategy on 11th grade students’ deep understanding of chemistry concepts, and (b) to explore the relationship between students’ understanding in chemistry and the development of basic systems thinking skills. For this purpose, an experimental group, taught by the SATL strategy, was compared with a control group taught by a traditional linear approach, regarding students’ chemistry understanding. For the intervention group, the relationship between students’ understanding and their systems thinking skills was also explored. The results indicated that chemistry understanding of students taught by the SATL strategy was significantly greater compared to that of students taught by a traditional linear approach. Moreover, a significant correlation was observed between students’ deep understanding of chemistry concepts and their systems thinking level. This research provides evidence for a possible relationship between chemistry deep understanding and the development of systems thinking skills.