Reflection plays a very important role in the learning process, contributing to improved learning performance and potentially influencing cognitive process. Few studies, however, have used computer-based mind mapping to enhance student reflective activities and examine the relationship between reflection, cognitive presence, and learning outcomes. Therefore, a quasi-experiment was implemented by recruiting students from a big data class at a normal university in central China. The collected data was analyzed by jointly using analysis of covariance, cognitive network analysis, linear regression, and moderating effect analysis. The results were as follows: (a) Students who used computer-based mind mapping performed better on reflection, higher-order cognitive presence, and learning outcomes. (b) The epistemic network analysis showed that students who used computer-based mind mapping had strong connections in higher levels of cognitive presence. (c) Reflection had a positive predictive effect on cognitive presence and learning outcomes, with mind mapping positively moderating the relationship between reflection, cognitive presence, and learning outcomes.