A Modified Sparsity Adaptive Stagewise Weak Orthogonal Matching Pursuit (MSASWOMP) algorithm is proposed to solve the problem of a priori sparsity and pilot resources for the actual underwater acoustic channel. Firstly, the initial sparsity estimation is used as the size of the initial support set, and the atom support set is obtained as the candidate set of backtracking screening by threshold weak selection of atoms. Then, the initial support set size is used as the initial condition value of backtracking to conduct secondary screening. Finally, the variable stage step size method is utilized to estimate the sparsity gradually and update the backtracking start condition value adaptively. The simulation results show that the proposed algorithm can obtain more accurate channel estimation with less pilot number, which can save pilot resources, and its Mean Square Error(MSE) is smaller than that of the traditional algorithm.