The invention discloses a method and a system for dividing submarine soil layer by pore water pressure static cone penetration, which relates to the field of soil layer dividing. The current stratification method in the CPTU index selection has a greater subjectivity, stratification results are not very accurate. The invention comprises the following steps: acquiring original index data, data processing, dimension reduction processing and clustering; based on the K-means clustering method, the self-encoder is used to reduce the dimension of the submarine pore pressure cone penetration test indexes, remove the redundant features, optimize the weights of the features, and cluster the subsets of the features by K-means. It is found that the outline coefficients and other clustering evaluationindexes of the cluster stratification results are greatly improved. The technical scheme utilizes a self-encoder combined with K-means clustering, the accuracy of the interface of the seabed soil layer is high, and the number of soil types, and the result display can be intuitively displayed.