Systems are an important part in today’s science education. Computer simulations have many advantages in teaching science systems. Our research goal is to test whether a hierarchical instructional scaffolding framework embedded in simulation-based learning environments and retrospective mental modeling task could facilitate mental model construction in learning science systems. This pilot study was conducted with a sample of adult learners who didn’t have strong science background. They were asked to learn ideal gas laws in a simulation-based environment. The results show that participants in the hierarchical scaffolding condition performed better than the non-hierarchical scaffolding condition. The retrospective mental modeling task could enhance learning only within the hierarchical scaffolding condition; while in the non-hierarchical scaffolding condition, the task was detrimental to learning. Based on the results from the pilot study, an 8 session curriculum teaching ideal gas laws to middle school students has been designed for our future study.