To improve the reliability and accuracy of the automatic enzyme immunoassay analyzer's micro-sampling system, a small autoinjection system was developed. A sophisticated injection arm was designed by the means of dislocation parallel distribution of the screw and injector piston rod. It possessed the function of pipetting, taking and removing the pipette tips. In the control system STM32 controller was used, controlling the single-axis S-type acceleration/deceleration algorithm and multithreaded coordinated motion. The acceleration/deceleration curves were analyzed and optimized by using the method of segmentation, the minimum injection rate of 1 μL was realized and the step rate was 0.05 μL. The position accuracy and the sampling precision of the injection system were verified by experiments, and the least squares linear fitting method was used to compensate the system sampling error. The results showed that the optimized S-type acceleration and deceleration algorithm could improve the motion characteristics of the stepping motor, avoiding the out-of-step and overshoot effectively, and the injection arm could reach a reliable position accuracy. The microinjection system had higher accuracy and stability after error compensation, at the test point 10, 50, 100 μL, the injection precision increased respectively from ±7.2%, ±5.3%, ±3.2% to ±1.8%, ±1.28%, ±1.15%. The system meets the miniaturization and high-precision design requirements, which has good application and popularization value.