The purpose of this study was to examine the effectiveness of online scaffolds in computer simulation to facilitate students' science learning. We first introduced online scaffolds to assist and model students' science learning and to demonstrate how a system embedded with online scaffolds can be designed and implemented to help high school students learn complex science concepts. The results showed that students were in favor of learning with the system. Additional findings from our qualitative data analysis revealed three major themes, including (a) supporting science learning with interactive simulation, (b) adopting data-driven strategies, and (c) generating naive and alternative conceptions. This finding has important implications for how online scaffolds should be designed and how to augment scientific inquiry and understanding with simulation-based learning. (Contains 4 figures.)