As part of geography education, geography courses play an important role in the development of spatial ability. However, how geography courses affect map-based spatial ability has not been well documented. In this study, we use an eye-tracking method to explore the impact of geography courses on map-based spatial ability. We recruited 55 undergraduates from Beijing Normal University (BNU) to attend the map-based spatial ability test before and after six-month geography courses arranged by the Faculty of Geographical Science, BNU. The results show that the participants’ map-based spatial ability significantly improved after taking the geography courses; specifically, accuracy increased by 22.3% and response time decreased by 14.7% after training. We analysed two types of eye-movement behaviour; in terms of processing measures, the fixation duration of the topographic map decreased by 18.4% and the fixation distribution was more concentrated after training, and in terms of matching measures, participants have more switch times per second for both photographed scenes and topographic maps. Switch times between options decreased by 48.2%, which is a notable decrease. These empirical results are helpful for the design of geography courses that improve map-based spatial ability.