The crustal motions throughout Germany have not yet been fully understood because the research scope of previous studies mainly focuses on some active grabens. Thus, we investigate it in detail to identify the neotectonic motion characteristics and specific deformation-ongoing regions. High accuracy for monitoring and data analyses is required because the expected crustal deformation in Germany is small. We use high-precision GNSS time series processing techniques and interdisciplinary data to reflect actual motions and determine the causes of deformation. Also, an advanced technique of discontinuity correction is introduced to unify the fragments of the GNSS coordinate time series for better velocity field reliability. Our findings show that the Earth’s crust in Germany tends to increase at a maximum speed of +1.0 mm/yr. Meanwhile, local subsidence of around -0.8 mm/yr is concentrated in the river basins (e.g., the Rhine, Ems, Elbe, Northern Oder, and Danube) and extensive mining regions. The Earth’s crust here also behaves with noticeable compressions. The intra-plate motion in Germany is ∼0.8 mm/yr. A special region with an extension rate of +4.3 nstrain/yr is observed along the North-South trending Regensburg-Leipzig-Rostock shear zone. Machine Learning clusters the 3D plate velocity field into three distinct regions with increasing speeds: Northwest, East, and Southwest. Significant surface deformations are detected mainly in the Upper Rhine Graben, Eifel volcanic field, and Thuringian-Vogtland slate mountains. The harmonic motions of the Earth’s crust in Germany have an amplitude of ∼4.7 mm, in which the surface loads contribute half to this type of motion. The findings will contribute to the overall picture of neotectonics here.