In the context of global digital transformation in education and post-pandemic reforms, online teaching has evolved from an emergency response into an essential instructional mode in higher education. Enhancing the quality of university students’ online learning and fostering their capacity for online deep learning (OnlineDL) have thus become key concerns in the educational field. Drawing on the extended Community of Inquiry (CoI) framework—which integrates teaching presence (TP), social presence (SP), cognitive presence (CP), and learning presence (LP, encompassing self-efficacy (SE) and self-regulated learning (SRL) as key antecedents of learner agency)—this study surveyed 3,167 Chinese university students and employed structural equation modelling to examine how these four core presences jointly facilitate OnlineDL. The results reveal that CP, LP (via its components SE and SRL), and TP exert significant and positive direct effects on OnlineDL.