The invention discloses a machine tool assembling joint surface design method capable of taking deformation error compensation as a target. The method comprises the following steps: in CAD (Computer Aided Design) software, according to statics analysis requirements and the structural characteristics of a machine tool, carrying out structure simplification; then, carrying out parameterized assembling on a machine tool entity model; importing the entity model subjected to the simplification and the parameterized assembling into finite element analysis software Ansys Workbench; creating a container capable of carrying out automatic analysis and extraction deformation by utilizing the software, carrying out orthogonalization of a processing spatial position and mesh generation, and meanwhile, finishing statics analysis and result storage; then, through data learning, obtaining the practical deformation amount of a machine tool assembling nominal joint surface under a situation that whole processing space deformation is considered; flipping the obtained practical deformation amount, adding the flipped amount and the nominal joint surface to serve as an actively designed machine tool assembling joint surface; and on the basis of a Monte Carlo method and a least square method, finishing profile tolerance design of the assembling joint surface with the combination of a data regression technology.