EarthView3D is the first worldwide orthographic stereoscopic 3D (S3D) map. It presents an accurate presentation of the Earth’s surface and can provide an immersive geospatial infrastructure for the upcoming metaverse ecosystems. This study conducted the first comprehensive assessment of the worldwide S3D maps, investigated the factors of visual discomfort, predicted discomfort level, and provided design recommendations for improving visual experience. Participants rated the S3D map images and reported the reasons for their visual discomfort. General Eye Symptom Questionnaires (GESQs) and Simplified Simulator Sickness Questionnaires (SSSQs) were used to record the development of visual fatigue with time. Six categories of measurable variables presumably related to visual discomfort were proposed based on participants’ reports, IEEE standards, and literature on visual experience. Factor analysis extracted four principal factors, disparity, terrain texture, luminance, and amplitude spectrum, whose contributions to variance were 38%, 23%, 16%, and 11%, respectively. The selected variables and subjective mean rating scores were used to construct a regression model for the prediction of visual discomfort. Performance evaluation Root Mean Square Error (RMSE) was lower than that reported in previous studies on different S3D databases. The results indicated that besides vergence-accommodation conflict and depth cue conflict, perception of Earth terrain’s textures and luminance played an important role in visual discomfort of viewing orthographic S3D maps.