A model differential settlement controlling device of a geotechnical centrifuge test. Composition of the model differential settlement controlling device is as below: two rows of support piers are fixed on one side of a model box bottom, and a dead flat on the two rows of support piers is supported by the support piers; two rows of elevators are fixed on the other side of the box bottom, and flange plates on upper parts of the elevators are fixed with a lifting plate; an embankment model is filled on the dead flat and the lifting plate; and elevators are connected with a step servo motor through a steering box arranged on the model box bottom, and the step servo motor is electrically connected with an external control system of the geotechnical centrifuge. According to the apparatus, accurate control of model differential settlement can be realized under a centrifuge running state, so as to master transmission and diffusion rules of nonuniform deformation of foundation in embankment soil filling and influences of the nonuniform deformation of foundation on characteristics of road bed nonuniform settlement, so as to provide reliable test basis for improving uniform transitioning technology of different structures in railway and road engineering.