Despite the increasing adoption of desktop virtual reality (VR) in higher education, the specific instructional efficacy of 3D interactive prompts remains inadequately understood. This study examines how such prompts—specifically dynamic spatial annotations and 3D animated demonstrations—influence learning outcomes within a desktop virtual learning environment (DVLE). Employing a quasi-experimental design integrated with eye-tracking and multimodal learning analytics, university students were assigned to either an experimental group (DVLE with 3D prompts) or a control group (basic DVLE) while completing physics tasks. Data collection encompassed eye-tracking metrics (fixation heatmaps, pupil diameter and dwell time), post-test performance (assessing knowledge comprehension and spatial problem-solving), and cognitive load ratings. Results indicated that the experimental group achieved significantly superior learning outcomes, particularly in spatial understanding and dynamic reasoning, alongside optimized visual attention patterns—characterized by shorter initial fixation latency and prolonged fixation on key 3D elements—and reduced cognitive load. Eye-tracking metrics were positively correlated with post-test scores, confirming that 3D prompts enhance learning by improving spatial attention guidance. These findings demonstrate that embedding 3D interactive prompts in DVLEs effectively directs visual attention, alleviates cognitive burden, and improves learning efficiency, offering valuable implications for the design of immersive educational settings.