In order to achieve low pulsation and high precision constant flow output of a series plunger infusion pump for HPLC, a flow control method based on S-curve for series plunger infusion pumps is proposed. Firstly, motion planning is carried out for the stepper motor. Secondly, the S-curve algorithm is used to achieve smooth driving of the plunger by the stepper motor. Finally, the feasibility of the proposed method is verified through motor operation tests and flow accuracy tests. The experimental results show that this method achieves constant flow and low pulsation output of the series plunger infusion pump, and using the S-curve control algorithm, the flow stability of the infusion pump is significantly improved, with an RSD of 0.055%.