Exact settlement measurement of substructures plays an important role in their status detection throughout all-life-cycle of high-speed railway. A Hydrostatic Pressure Difference Levelling system (HPDL) is developed based on the mechanism that pressures of any two points at different elevations in incompressible static liquid are different. The approach accounts for a hyperbolic variation in the density of the pressure transmission liquid with temperature, variation in the earth’s gravitational field and the elevation at the measurement point. High accuracy capacitive differential pressure transmitters are adopted owing to their high sensitivity, temperature-insensitive, low energy consumption, and sensing stability. The HPDL results are verified with settlement values measured by the precise level. It was demonstrated that the HPDL results correlate well with the precise level and can be considered as an effective method to measure the settlement of high-speed railway substructures.