The ongoing collision between the Indian plate and the Eurasian plate brings up N-S crustal shortening and thickening of the Tibet Plateau, but its dynamic mechanisms remain controversial yet. As one of the most tectonically active regions of the world, South-Eastern Tibet (SET) has been greatly paid attention to by many geoscientists. Here we present the latest three-dimensional GPS velocity field to constrain the present-day tectonic process of SET, which may highlight the complex vertical crustal deformation. Improved data processing strategies are adopted to enhance the strain patterns throughout SET. The crustal uplifting and subsidence are dominated by regional deep tectonic dynamic processes. Results show that the Gongga Shan is uplifting with 1-1.5 mm/yr. Nevertheless, an anomalous crustal uplifting of ~8.7 mm/yr and negative horizontal dilation rates of 40-50 nstrain/yr throughout the Longmenshan structure reveal that this structure is caused by the intracontinental subduction of the Yangtze Craton. The Xianshuihe-Xiaojiang fault is a major active sinistral strike-slip fault which strikes essentially and consistently with the maximum shear strain rates. These observations suggest that the upper crustal deformation is closely related with the regulation and coupling of deep material.