To explore a flexible control and design scheme in the field of stepper motor control, a RISC-V microcontroller for stepper motor control was designed and developed, based on the open source innovation of the RISC-V (reduced instruction set computer-five) architecture in the hardware field. By integrating the processor, memory, peripherals and debugging interface modules into a single FPGA (field-programmable gate array) chip, the configurable microcontroller platform was constructed. By building simulation debugging environment and joint debugging of software and hardware, the correctness of microcontroller design was verified. In the test of stepper motor control system, pulse width modulation (PWM) module produced control pulses, quadrature coded pulse circuit (QEP) detected position of the rotor, the hardware system worked normally and the relative error of the experiment was controlled in the order of one thousandth.