A pressure force control system for hot embossing of microfluidic chips is designed with a moment motor and a ball bearing lead screw. Based on the numeric PID technique, the algorithm of pulsant integral accelerated PID control is presented and the negative effects of nonlinearity from friction, clearance and saturation are eliminated. In order to improve the quick-response characteristic, independent thread technique is adopted. The method of pressure force control based on pulsant integral accelerated PID control and independent thread technique is applied with satisfactory control performance.