The invention discloses a method for simulating rock masses with surfaces of unconformity. According to the method, the influence of the surfaces of unconformity of rock stratums on simulation is taken into account, PFC3D based on the particle flow code theory is used as a simulation platform, and contact situations of the different rock stratums in the underground rock masses are simulated respectively, wherein the contact situations comprise conformity, parallel unconformity and angular unconformity. The method includes the following steps that a rock mass coordinate system is defined, key coordinate points of the trend of contact surfaces are determined, trend curves are fitted through MATLAB, curve parameters are acquired, the rock stratums are constructed through a drop method, and the contact surfaces are formed through FISH according to the parameters of the trend curves. By the adoption of the method, the underground rock masses can be accurately modeled, and the method is used for constructing the rock masses mingled with the contact surfaces of different forms.