In the area of underwater communications, MIMO(Multiple Input Multiple Output) techniques for increasing the data rates are being studied. The advantage of MIMO techniques is increasing channel capacity, and it does not use additional frequency or transmit power. Representative method is V-BLAST. The channel estimation is one of important roles in MIMO system. In this thesis, the channel estimation method for underwater MIMO communication system is proposed. The proposed method is comprised of channel tap position detection based on L1-norm minimization, channel regeneration, and LMS(Least Mean Square) channel estimation. To prove the performance of the proposed method the simulations are conducted. The number of transmitters and receivers is 2, respectively. The channels for simulation were generated by Bellhop model, and the sound speed profile that was really measured in Korean East Sea was used. The range between sources and receivers is 1 km, and the water depth is 200 m. In simulation results, the channel tracking speed of the proposed method is faster than the conventional method. The BER(Bit Error Rate) performance improves about 10%. In the future, it is needed to prove the performance of MIMO underwater communication via sea trials.