This study examined and compared the effects of two types of online peer assessment, namely, "free selection and invitation" (FS&I) assessment and the commonly implemented "assigned-pair" (AP) assessment, on undergraduates' research competencies, flow, motivation, and interaction, supported by the Cloud Classroom online learning system. Ninety-three undergraduates from a research methods course participated in this study. They were randomly divided into two groups: an FS&I group and an AP group. The two groups experienced exactly the same teaching conditions except for different online peer assessment types. The study was conducted over one semester (16 weeks). Both quantitative and qualitative methods were used to examine the effects of the two types of online peer assessment. Regarding research competencies that were represented by conceptual knowledge and research proposal, this study found that the FS&I and AP groups showed no significant difference in conceptual knowledge score, and that the FS&I group performed significantly better in the quality of research proposals than the AP group. The FS&I group also manifested higher levels of flow and motivation than the AP group. Additionally, social network analysis (SNA) revealed that the FS&I group exhibited more interactions and closer connections with peers than the AP group. These results suggest that FS&I online peer assessment is an effective scaffolding that can improve undergraduates' research competencies, learning engagement and willingness to interact. The implications of this study are also discussed.