In the analysis of a large seepage system,the total water transmission matrix is symmetric,large and sparse,so the data storage algorithm of total water transmission matrix is the key factor for the total amount of data storage.In this paper,a new one dimension compressing data storage algorithm of the matrix is present in combination with preconditioned conjugate gradient(PCG) method,and also,the formulas and the calculating process for this algorithm are discussed.The calculation of an engineering case shows that the one dimension compressing data storage algorithm combined with PCG approach can reduce calculation time remarkably and calculation cost.