The use of high-precision technology of the global navigation satellite system (GNSS) has put forward the task of developing the methods for the creation and the use of a new national open coordinate system in the Republic of Uzbekistan. In the country, up to now the CS42 coordinate system, based on the Krasovsky ellipsoid used for geodetic works. The Baltic normal system of heights (1977), tied to the mean sea level with the zero mark of the Kronstadt tide gauge, was adopted as a height datum. Due to lack geoid information for the territory of the country determined by modern methods, the realization of a height reference datum becomes an urgent task. The results of GPS measurements usually presented in a coordinate system relative to the WGS-84 ellipsoid, and have to convert to national, local coordinate systems to solve practical problems. The horizontal GPS coordinates can directly use for computational work, but the geodetic heights have to convert to orthometric (or normal) heights for a given area using geoid information. In this work, a study was made of methods for updating the height reference datum of topographic maps at a scale of 1:200,000 using a deformation matrix between two reference coordinate systems for the territory of the Fergana Valley. To convert between geodetic and normal heights between the CS42 and WGS84 coordinate systems, a vertical deformation matrix in the GTX format of the National oceanic and Atmospheric Administration of Canada (NOAA) have created. To create a file of elevation displacements, the results of classical leveling and satellite GPS measurements have used at 144 “common” points of the entire network of the country with known coordinates in two systems. The difference between the “real” values of geodetic heights obtained from GPS measurements and “modeled” ranges from -0.13 m to 0.67 m. It has revealed that the maximum differences in heights are in the area of the Fergana basin itself and may be a consequence of both an anomalous gravitational field in this part of the territory, and an insufficient density of stations of the GPS network in the northeastern part of the area. The normal height values for the updated topographic map in WGS84 have computed using the EGM2008 high precision geopotential model. The discrepancy between the values of heights in CS42 and WGS84 is in the range of -3.93 m and 0.31 m.