Extant literature has preliminarily confirmed the potential benefits of holographic projections for educational purposes. Yet, students' experiences of learning by holographic projection have rarely been addressed. The main purpose of this study was therefore to explore students' conceptions of and approaches to learning by holographic projection. A holographic projection system was devised to assist students in learning the concept of lunar phases. This study also investigated the relationships between students' conceptions and approaches, and determined if there were any variations based on students' learning gains. Phenomenographic analysis was adopted to analyze 30 university students from Taiwan, and a multiple-choice conceptual test was conducted to assess their learning achievements. The main findings indicated that students with conceptions of learning by holographic projection as increasing the presence of a scene or mapping 2D images to 3D structures tended to adopt surface approaches, such as only observing the changes presented in the holographic projection, repetitively operating the system functions without intended purposes, or simply following the instruction guidelines to meet the minimal requirements. However, this study unexpectedly found that students who utilized surface approaches had significantly higher learning gains on the conceptual test than their counterparts did.