Massively open online courses (MOOCs) offer learners opportunities for self-improvement and knowledge development. Linking cognitive processes and learning outcomes is helpful in supporting students learning with the help of MOOCs. Based on the cognitive presence of the Community of Inquiry framework, this study quantified the effect of cognitive presence on students' learning performance by analysing more than 400,000 posts of 13 MOOCs. First, the study built a highly predictive classification model using a machine learning algorithm to automatically identify the phases of cognitive presence in MOOC forum posts. Subsequently, multilevel modelling was used to analyse the influence of learners' cognitive presence on their learning performance. The results showed that different phases of cognitive presence influenced students' learning differently. The findings help us understand the phases and depth of students' cognitive presence and can be used as the basis for MOOCs to automatically provide appropriate cognitive feedback and support to students.