Dynamic errors of the stylus-based probing system seriously affect the measurement accuracy in surface quality detection on microstructures. A method, which is focused on measuring the surface form of microgears, microholes on the injector nozzle, and so forth, is proposed to control dynamic errors of the stylus-based probing system. Firstly, two kinematical models were built to systematically investigate the dynamic performance of the stylus-based probing system, and the relationship between the measuring force, scanning speed, fidelity, and dynamic errors was described. Then, numerical simulations of the surface form measurement, in which a sine-shaped microstructure was taken as a target surface, were carried out. Results of the numerical simulations reveal that the dynamic errors were affected by the scanning speed and the initial position of the measured specimen. Lastly, a method to control dynamic errors by properly setting up the scanning speed and the initial position of the specimen was proposed for the surface form measurement of microstructures.