For the construction of a Glass Earth a 3D geological entity model needs to be loaded into a Digital Earth visualization engine to visualize the expressions of geological entities. Space expressed by a 3D geological entity model is formed by a research area that extends vertically to a certain depth range in a projected coordinate system. When a 3D geological entity model is loaded into Digital Earth, the model-bounding box is combined with the model’s central point to perform the transformation, which causes the boundaries of adjacent models to deviate from each other to various degrees. Moreover, gaps and overlaps form at the top and bottom of the models, respectively. In this study, based on analyses of elevation naturalization correction and Gaussian projection deformation characteristics, bounding box–based free-form deformation was used to realize the model transformation in the process of loading a complex 3D geological entity model. By establishing a parametric model and mapping its relationship to the object to be deformed, free-form deformation was used based on deformation error correction. In this way, deviations between 3D geological entity models loaded into Digital Earth can be reduced. Using practical project cases, 3D geological entity models located at the margin of a zone six degrees wide in longitude and their central regions were comparatively analyzed. The results show that the free-form deformation used in this study can effectively reduce deviation problems in models.