While prior research has revealed the promising impact of concept mapping on learning, few have comprehensively modeled different cognitive behaviors during concept mapping. In addition, existing concept mapping tools lack effective feedback to support better learning behaviors. This work presents MindDot, a concept map-based learning environment that facilitates the cognitive process of comparing and integrating related concepts via two forms of support, a hyperlink feature and an expert template. Study results suggested that the hyperlink support had a positive impact on the development of comparative strategies and enhanced learning, while the template support had marginal effects on learning. We further evaluated the cognitive process at a fine-grained level with two forms of visualizations. We then extracted several behavioral patterns that provided insights about the cognitive process in learning. Lastly, we derive design recommendations that we hope will inspire future concept map-based learning systems that evaluate students’ learning processes and adaptively support them in developing effective learning behaviors.