Argumentation scaffolding can be used to enhance the formulation of logical arguments as well as the performance of such arguments. This study presents a web-based synchronized scientific argumentation environment integrated with prompt scaffolding to support simulation-based physics learning for elementary school students. To investigate the effects of prompt argumentation scaffolding, two sixth-grade classes totaling fifty-five students worked in small groups to complete a simulation-based physics learning activity regarding the principle of leverage. One class was allocated to an experimental group that received prompt argumentation scaffolding, whereas the other class was assigned to be the control group not receiving prompts. Learning achievements such as science conceptual understanding and scientific explanation skills were examined, and lag sequential analysis (LSA) was used to compare the argumentative behavioral patterns of the two groups. The results showed that the students in the experimental group outperformed those in the control group in terms of their capacity to produce scientific explanations, though no significant difference in their understanding of physical concepts. Furthermore, the LSA results revealed that the experimental group demonstrated more coherent, evidence-based arguments and conscious reasoning, whereas the control group displayed more of a conversational tone and was unstructured in its debates with others.