The purpose of this study was to qualitatively explore how students experienced the MOOC-based flipped learning and how should different scaffolding be emphasized in different stages in such educational contexts through the lens of the revised community of inquiry (CoI) framework. In total, 22 first-year undergraduate students were invited for one-on-one in-depth interviews. The results indicated that MOOC-based flipped learning allowed students to experience all four types of presences outlined in the revised CoI framework. In terms of each presence, students highlighted that the MOOC-based flipped course provided more learning presence in the form of monitoring and strategy, greater cognitive presence through integration, more social presence through affective expression and open communication, and increased teaching presence through enhancement of direct instruction and assessment during both online and in-class sessions. And the challenges of implementing MOOC-based flipped learning in university courses were also mentioned ranging from the need for group cohesion in in-class learning designs, the necessity of helping students improve planning, triggering events, to the enhancement of design, and organization between MOOCs and the existing formal curricula. The findings have implications for practitioners who hope to build an integrated learning experience around MOOCs.