Applications of optical clocks in physical geodesy for determining geopotential are of increasing interest to scientists as the accuracy of optical clocks improves and the clock size becomes more and more compact. In this study, we propose a data processing method using the ensemble empirical mode decomposition technique to determine the geopotential difference between two sites in Wuhan based on the frequency comparison of two optical clocks. We use the frequency comparison record data of two Ca+ optical clocks based on the optical fiber frequency transfer method, provided by the Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences (Wuhan, China). By optical clock comparisons we obtained a geopotential difference of 42.50 ± 1.03 m2 s−2 (equivalent to height difference of 4.33 ± 0.11 m) between the two sites, which is excellent compared to the geopotential difference of 42.56 ± 0.29 m2 s−2 (equivalent to height difference of 4.34 ± 0.03 m) measured by a spirit leveling. The results show that the optical fiber frequency transfer method is promising in determining the geopotential and potential for unifying the world height system.