The purpose of this study was to investigate the impacts of visual cues and different types of self-explanation prompts on learning, cognitive load and intrinsic motivation, as well as the potential interaction between the two factors in a multimedia environment that was designed to deliver a computer-based lesson about the human cardiovascular system. A total of 126 college students were randomly assigned in equal numbers (N = 21) to one of the six experimental conditions in a 2 X 3 factorial design with visual cueing (visual cues vs. no cues) and type of self-explanation prompts (prediction prompts vs. reflection prompts vs. no prompts) as the between-subjects factors. They completed a pretest, subjective cognitive load questions, intrinsic motivation questions, and a posttest during the course of the experience. A subsample (49 out of 126) of the participants' eye movements were tracked by an eye tracker. The results revealed that (a) participants presented with visually cued animations had significantly higher learning outcome scores than their peers who viewed uncued animations; and (b) cognitive load and intrinsic motivation had different impacts on learning in multimedia due to the moderation effect of visual cueing. There were no other significant findings in terms of learning outcomes, cognitive load, intrinsic motivation, and eye movements. Limitations, implications and future directions are discussed within the framework of cognitive load theory, cognitive theory of multimedia learning and cognitive-affective theory of learning with media.