Concept map (CM) is introduced as a useful tool for studying students' system thinking (ST). However, it is more known to represent students' knowledge of system components and organization and less recognized as a tool to examine and enhance students' understanding about the underlying causal mechanisms in complex systems. In this study, through a mixed method approach, we investigated the potential of CM in demonstrating undergraduate students' (n = 173) ST. We also conducted a comparative analysis to examine the effects of different scaffolding on developing students' ST skills. Through a theoretical framework of causal patterns, we present a new perspective on what CM reveals about students' ST and what are its limitations in showing system complexities. The results indicated that CM can provide a platform for students to practice causal mechanisms such as domino, mutual, relational, and cyclic causalities, and accordingly, work as a tool for teachers to examine students' knowledge of such mechanisms. The results also showed that students improved in demonstrating ST by CM when they were scaffolded for showing causal mechanisms and building CM. Eventually, this study concludes that the CM is a highly relevant tool to increase and examine students' ST skills. To this end, we found it is important to explicitly teach students about causal patterns and guide them to construct CM with an emphasis on showing the interconnection among concepts.