This study focuses on the investigation of the effects of computer simulation and animation (CSA) on students' cognitive processes in an undergraduate engineering course. The revised Bloom's taxonomy, which consists of six categories in the cognitive process domain, was employed in this study. Five of the six categories were investigated, including remember, understand, apply, analyze, and evaluate. Data were collected via a think‐aloud protocol involving two groups of student participants: One group learned a worked example problem with a CSA module, and the other group learned the same problem with traditional textbook‐style instruction. A new concept called frequency index was proposed for use in qualitative research that involves the quantitative comparison of the overall popularity of a particular mental activity performed by two groups of students. The results show that as compared to traditional textbook‐style instruction, CSA significantly increases students' activities in the understand category of the revised Bloom's taxonomy during learning and significantly increases students' activities in the understand, apply, analyse, and evaluate categories during subsequent problem‐solving. That learning via CSA has a profound impact on subsequent problem‐solving is attributed to intensive human–computer interactions built in the CSA learning module.