The application of Computer Simulation and Animation (CSA) in the instruction of engineering dynamics has shown a significant growth in the recent years. The two foremost methods to evaluate the effectiveness of CSA tools, including student feedback and surveys and measuring student change in performance, suggest that CSA modules improve student learning in engineering dynamics. However, neither method fully demonstrates the quality of students’ cognitive changes. This study examined the quality of effects of application of CSA modules on student learning and problem solving in particle dynamics. It also compared CSA modules with textbook-style problem-solving regarding the changes they cause in students’ cognitive process. A qualitative methodology was adopted to design and implement a study to explore the changes in participants’ learning and problem-solving behavior caused by using a CSA module. Collected data were coded and analyzed using the categories of cognitive process based on the Revised Bloom’s Taxonomy. An analysis of the results revealed that the most significant effects were observed in understanding, analyzing, and evaluating. The high frequency of “inference” behavior after working with modules indicated a significant increase in participants’ understanding activity after working with computer modules. Comparing behavior changes of computer-simulation group students with those who worked with a textbook-style example demonstrated that the CSA modules ignited more analytical behavior among students than did textbook-style examples. This study illustrated that improvement in learning due to the application of CSA is not limited to conceptual understanding; CSA modules enhance students’ skills in applying, organizing, and evaluating as well. The interactive characteristics of CSA play a major role in stimulating students’ analytical reasoning and critical thinking in engineering dynamics.