Abstract: The engineering effect of endogenic processes in Himalayan orogen is a frontier problem of basic scientific research in the field of geosciences and engineering. In the longitude direction, based on the tectonic and lithological differences, the Himalayan orogenic belt is divided into 3 parts: Tethys Himalaya, Higher Himalaya and Lesser Himalaya. These studies reveal the universal law that the engineering geological characteristics and disaster effects of the different parts are restricted by endogenic processes. This paper presents the following arguments. Firstly, the rapid uplift of Higher and Lesser Himalaya under the mechanism of compressional collision and orogeny, the earthquakes are mainly thrust fault type and have high earthquake intensity and high frequency. The dominant direction of geostress is close to NE-WS. The terrain develops to a large height difference. The river cuts strongly. The Mountain disaster is serious. Secondly, the Tethys Himalaya belongs to the detachment system and is in a relatively subsidence state. The earthquakes are mainly normal fault type. The seismicity is relatively weak. The geostress direction is close to the E-S. The terrain evolution is trending towards weakening the terrain. And the avalanche disaster is serious. Lastly, the marine glacial landforms, glacial lakes and glacial debris flows are unique to the Higher Himalaya. These may be important issues in controlling the trans-Himalayan railway line scheme. According to the understanding that there are significant differences in the engineering effects of the above parts, this paper puts forward the suggestion of taking the structural division as the railway engineering geological zoning. Taking the traffic corridor of the proposed China-Nepal railway as an example, the engineering geological zoning map is drawn. The research is helpful to advance the theory of Himalayan orogen to the level of engineering application. At the stage of railway large-scale scheme comparison and selection, it provides a new way to obtain information in wide area, high efficiency and low cost.