Deepwater riser is an important weapon for deepwater oil and gas exploration, and it is the most challenging part of deepwater oil and gas development technology. Along with the continuous development of the offshore oil, the fatigue monitoring technology of the deep water riser plays an important role in the prevention of the water pipe accidents. However, ocean current velocity is one of the important reasons leading to the fatigue of deep water. In order to monitor ocean velocity is commonly used in situ monitoring of ocean currents. However, there is a defect in this method: Because of the dynamic response of the riser, especially the existence of the wake region, there are some errors in the measurement of ocean current velocity. According to the characteristics of the wake flow, the flow velocity measurement principle and the operating environment characteristics of the pipe, a new method for compensating the velocity of the MEMS three axis accelerometer and gyroscope is proposed.