According to Einstein’s general relativity theory, a precise (atomic) clock runs faster at a position with higher gravitational potential than a clock at a position with lower potential. Here, we provide a direct clock comparison using a fixed hydrogen clock and a portable hydrogen clock for geopotential determination based on the two-way satellite time and frequency transfer (TWSTFT) technique. After synchronizing the two hydrogen clocks at positions at the same height, the clocks were compared for a height difference of 22 m over a period of 14 days using the TWSTFT technique. Interpretation of the observed time elapse implies a height difference of 175 m +/- 59 m, which matches the frequency stability of our instruments. This study and relevant experiments provide a way of determining the geopotential using ultra-high precise clocks based on the TWSTFT technique in the near future.