Although the learning of programming language is critical in science and technology education, it might be difficult for some students, especially novices. One possible reason might be the fact that programming language, especially for three-dimensional (3D) applications, is too complex and abstract for these students to understand. Programming for 3D applications requires understanding the spatial relationship of 3D objects and hence needs a visualization technique more. In view of this, this article presents an augmented reality (AR)-enhanced learning system that offers visual representation and interactivity to help students learn programming for 3D applications. To examine the influences of such an AR-enhanced system on student learning, a within-group experiment with 34 college students was conducted. All students used both of an AR-enhanced version and an ordinary version. The findings revealed that the AR-enhanced version made students have better learning efficiency than the ordinary system. In addition, the AR-enhanced system also made students have enhanced perceptions in terms of system usability, flow experience, and usage perception. Based on the results, further development of AR-enhanced learning systems is also suggested and discussed.