Secondary-level students encounter many difficulties in learning complex systems with hierarchical levels. Scaffolding is very critical in teaching complex systems. We have two complementary research questions on scaffolding: 1. How can we chunk and sequence the learning activities in teaching complex systems? 2. How can we help students make connections across system levels? A simulation-based environment teaching a chemical system was used as the research instrument, and the study was conducted at a middle school setting. The results showed that the sequencing method following the “from concrete to abstract” principle produced better recall and comprehension of the system concepts (knowledge integration), while the sequencing method aligned with the casual structure of the system facilitated the construction of a better causal model for transfer. The results also demonstrated that explicit level-bridging scaffolding had positive effects on both knowledge integration and learning the deep causal structure.