This paper proposes a high-precision real-time correction sounding system using Micro Electro Mechanical Systems (MEMS) inertial measurement units, which can correct the effective depth from the sea surface to the seabed in real-time. The advantages of the proposed system are as follows: (1) The system outperforms a single-beam sounder available on the market in that the range of depth errors caused by the swing of a research vessel is about 2%: (2) Since the proposed system is small compared to the existing attitude and heading reference system, it can be employed for unmanned surface vehicle, remotely operated underwater vehicle, autonomous underwater vehicle, and so on. Experimental results show that an attitude, heading and depth measured by the developed system are within the acceptable range, and the system can give a stabilized attitude, heading and depth information for a long time.