The Republic of Uzbekistan currently uses the Baltic normal system of heights associated with the quasi-geoid surface. The introduction of innovative technologies of global navigation satellite systems (GNSS) made it possible to determine with high accuracy the geometric heights related to the Earth model — an ellipsoid. For a complex representation of spatial data and analysis of information about the territory, natural resources, man-made objects, their dynamics in the National Geographic Information System (NGIS), first of all, it is necessary to solve the problem of refining the reference vertical coordinate system and ensuring its connection with the global ones, namely, to ensure adjustment of these two height systems. The task is complicated by the fact that for the territory of the country there is no information about the quasi-geoid determined by modern methods, which are necessary for the transition from geometric ellipsoidal heights obtained using GPS measurements to normal heights which are used for solving a wide range of practical problems in various fields of environmental sciences. In recent years, global geopotential models of the Earth (GGM) calculated using various satellite missions has become an alternative solution to the problem. The study considers two high order GGMs (EGM2008 and GECO) to create a system of normal heights for the territory of the Fergana Valley. The height anomaly values for them reach the maximum for the region — about −49 m. The method of constructing parametric models (or corrective surfaces) using leveling and GPS measurements at “common points” was used to refine them. The range of corrections made was from −0.28 m to 0.29 m. Moreover, the GECO model was significantly improved compared to EGM2008 in the flatland part of the study area, which has large geoid anomalies. The Krasovsky ellipsoid and the corresponding Baltic height system were chosen as a reference surface to create in the future a grid for converting heights between local and geocentric coordinate systems. The results of a comprehensive statistical analysis made it possible to reveal that GECO gives a more accurate representation of the region’s relief and is recommended for solving practical problems in the Fergana Valley.