Regulations between pre-estimated channel length and estimation precision were analyzed. The estimation quality was evaluated in time using statistics of the equalized signals which can help adjust the length of channel estimation algorithm automatically. In view of the differences among subcarriers caused by underwater acoustic channels, a new algorithm which realized optimum rate and power assignments based on channel estimating results was put forward. Compared with the traditional algorithm which assigned rate and power equally to each subcarrier, the new algorithm achieved better property of bit error rate. Simulations and experiments validate the effectiveness and correctness of the researching contents. 