In response to the demand for low resource consumption, parallel control, and real-time response to target position changes in precision measurement and manufacturing of multi-axis stepper motor controllers, this paper proposes a field programmable gate array-based method for generating trapezoidal velocity profiles and pulse generation, which can easily keep parallelism and independence during multi-axis control. By avoiding using multiplication and division, this controller not only reduces resource consumption but also enhances the pulse output frequency. To address the real-time responsiveness of the velocity profile generation algorithm to changes in the target position during the control process, the algorithm introduces a novel real-time comparative state transition logic for speed control, which makes it capable of adjusting the acceleration within a single clock cycle, enabling its application in scenarios that require higher levels of real-time performance. Finally, the designed controller is applied to a four-axis positioning system for performance validation.