This study extends the community of inquiry (CoI) framework and empowerment theory by exploring the relationships between motivational variables, CoI variables, learning presence, and empowerment. We added motivational beliefs (growth mindset, self-efficacy, and task value) as associated variables and learning presence (online self-regulation) as a mediator and examined their contribution to students' cognitive presence and empowerment. The participants were 539 junior middle-school students in rural China who had acquired significant online learning experience as a result of the COVID-19 pandemic. The results showed that motivational variables were associated with students' social presence and online self-regulation, which in turn related to their cognitive presence and empowerment in the online learning environment. Growth mindset and self-efficacy also exhibited a significant correlation with students' cognitive presence. There was a positive correlation between cognitive presence and empowerment. We also found teaching presence has a positive association with social presence but a negative association with online self-regulation. Our research provides a more comprehensive explanatory model of online instruction and student empowerment by introducing the elements of motivational beliefs and learning presence to the CoI framework.