The invention discloses a modeling method for a three-dimensional rock block system. The modeling method includes the following steps: A, inputting triangles that represent boundaries of a rock engineering model and determine geometric parameters of random structured surfaces, and establishing topological access relationships among sides, edges and points of the triangles; B, calculating intersecting lines of all the sides in the space; C, conducting line segment coplanar identification through a recursion algorithm; D, calculating intersecting lines of all the line segments in the space; E, identifying closed loops on all the sides in the space; F, analyzing inclusion relationships among the closed loops; G, updating the topological access relationships among the sides, the edges and the points; H, cancelling isolate polygon sides in the space, and generating twin sides of non-isolate polygon sides; and J, identifying all three-dimensional rock blocks in the space through geometric topology analysis; and analyzing inclusion relationships among the blocks. All-space identification of a three-dimensional complex block system is realized through geometric topology correlation analysis of points, lines, sides and bodies in a rock structured surface network. The method is easy to operate, and the analysis precision is high.