In view of how to choose the prestressed anchor cable layout of Baihetan bottom holes, this paper analyzed stress and displacement of Baihetan 6# bottom hole with different U-shaped prestressed anchor cable layout schemes using three-dimensional finite element sub-model method, which preliminarily drafts two layouts. The stress and displacement of the typical sections and points was analyzed to determine the safety of the structure in the process of different prestressed anchor cable layout. The results showed that there is no non-uniform distribution and mutation of displacement in the pier and girder structure in the process of different prestressed anchor cable layouts, which is in line with the engineering experience and stress standards, and the security performance of scheme one is slightly better than that of scheme two. The results can provide a reference for the design of anchor cable of the large thrust prestressed gate pier.