In online STEM courses, self-regulated learning (SRL) serves a critical role in academic success because students are required to monitor and regulate their learning processes. Yet, relatively little research has investigated which and to what extent do SRL strategies contribute to students' online learning experiences. In this paper, with a lens of the Community of Inquiry (CoI) framework (Garrison et al., 2001), we investigated which students' SRL strategy use predicts three elements of the perceptions of CoI: teaching, social, and cognitive presences. Our sample included 278 undergraduate STEM students who enrolled in a self-paced online course teaching the introductory level of calculus. A Multiple Indicator-Multiple Cause (MIMIC) analysis was employed to investigate the SRL predictors that affect three elements of CoI. Prior to MIMIC analyses, we confirmed the dimensionalities of the SRL and the perceptions of CoI, respectively, through a series of confirmatory factor analyses (CFAs). The MIMIC analysis revealed that environmental structuring and help-seeking affected teaching presence. Social presence was predicted by goal setting and self-evaluation through peers, whereas environmental structuring, time management, and self-evaluation through peers predicted cognitive presence. The findings of this study provide new empirical evidence on the different roles of SRL in promoting three elements of the perceptions of CoI. Academic and practical implications of the findings of the study were discussed.