Previous studies have suggested that students perform better in certain qualities of the argumentation skills with scaffolding. Moreover, many researchers have proposed that students' conceptions may be related to the progress of learning activity. To investigate the effects of scaffolding and students' conceptions, two studies were conducted in an online argumentation environment, namely iArgue. The result of study 1 indicated that providing scaffolding may improve only students' argumentation skills at lower levels (i.e. claims and grounds), but not their argumentation skills at higher levels (i.e. warrants, backings, and rebuttals). The outcome of study 2 inferred that students who perceived higher goal and more sophisticated process of online argumentation had better argumentation skills at higher levels. The interaction effects of scaffolding and students' conceptions were further probed and concluded that the effects of students' conceptions did not depend on scaffolding tools. Further implications were discussed in the paper.