This paper presents a research model to evaluate the usability of computer-mediated learning technology, user acceptance of the technology, and the effect of the technology on learning outcomes. We also introduce the use of innovative research techniques for the evaluation, including eye tracking and think-aloud protocol. Think-aloud protocol allows us to understand a user’s state of mind while he/she is interacting with the system. Eye tracking also provides additional insights into a user’s cognitive state while using the system. Both qualitative and quantitative data can be collected following the research model, thus providing more in-depth understanding on the effect of the system. We demonstrated the application of the research model and research techniques in evaluating visualization software designed in a project funded by the National Science Foundation.