Complex systems are an important topic in science education today, but they are usually difficult for secondary-level students to learn. Although graphic simulations have many advantages in teaching complex systems, scaffolding is a critical factor for effective learning. This dissertation study was conducted around two complementary research questions on scaffolding: (1) How can we chunk and sequence learning activities in teaching complex systems? (2) How can we help students make connections among system levels across learning activities (level bridging)? With a sample of 123 seventh-graders, this study employed a 3x2 experimental design that factored "sequencing methods" (independent variable 1; three levels) with "level-bridging scaffolding" (independent variable 2; two levels) and compared the effectiveness of each combination. The study measured two dependent variables: (1) "knowledge integration" (i.e., integrating and connecting content-specific normative concepts and providing coherent scientific explanations); (2) "understanding of the deep causal structure" (i.e., being able to grasp and transfer the causal knowledge of a complex system). The study used a computer-based simulation environment as the research platform to teach the ideal gas law as a system. The ideal gas law is an emergent chemical system that has three levels: (1) "experiential macro level" (EM) (e.g., an aerosol can explodes when it is thrown into the fire); (2) "abstract macro level" (AM) (i.e., the relationships among temperature, pressure and volume); (3) "micro level" (Mi) (i.e., molecular activity). The sequencing methods of these levels were manipulated by changing the order in which they were delivered with three possibilities: (1) "EM-AM-Mi;" (2) "Mi-AM-EM;" (3) "AM-Mi-EM." The "level-bridging scaffolding" variable was manipulated on two aspects: (1) inserting inter-level questions among learning activities; (2) two simulations dynamically linked in the final learning activity. Addressing the first research question, the Experiential macro-Abstract macro-Micro ("EM-AM-Mi") sequencing method, following the "concrete to abstract" principle, produced better knowledge integration while the Micro-Abstract macro-Experiential macro ("Mi-AM-EM") sequencing method, congruent with the causal direction of the emergent system, produced better understanding of the deep causal structure only when level-bridging scaffolding was provided. The Abstract macro-Micro-Experiential macro ("AM-Mi-EM") sequencing method produced worse performance in general, because it did not follow the "concrete to abstract" principle, nor did it align with the causal structure of the emergent system. As to the second research question, the results showed that level-bridging scaffolding was important for both knowledge integration and understanding of the causal structure in learning the ideal gas law system. [The dissertation citations contained here are published with the permission of ProQuest LLC. Further reproduction is prohibited without permission. Copies of dissertations may be obtained by Telephone (800) 1-800-521-0600. Web page: http://www.proquest.com/en-US/products/dissertations/individuals.shtml.]