The wave measurement system can automatically monitor the wave height, period and direction of the ocean in a fixed area, all weather and all day. A wave measurement system based on STM32F429 processor and MTI-3-8A7G6T inertial sensor is designed. The algorithm and software design of the wave measurement system were completed, in which the wave height and wave period were measured by integrating the acceleration twice in the frequency domain, which could effectively avoid the influence of the DC component on the integral result. Meanwhile, the digital filtering was carried out in the frequency domain to filter out the zero deviation error of the accelerometer and the random noise of low frequency. The measurement of wave direction is obtained from the Angle between horizontal resultant acceleration and magnetic heading. The wave measurement algorithm is successfully transplanted into STM32F429 processor through software design to realize the wave measurement function. Experimental results show that the measurement errors of the wave measurement system are within the specified range for waves with different wave heights and wave periods. The system can solve the wave characteristic value accurately. run stably for a long time. and meet the requirements of high precision and high reliability.