A rock mass is composed of blocks, and the interfaces of various scale blocks represent different kind discontinuities. Such structure is also associated with nonuniformity of stresses. The stress–strain behavior of rock mass in the Khibiny apatite–nepheline massif in the course of mining is governed by natural geological and induced faulting. This study considers modification of the finite element method in the stress–strain analysis of rocks with regard to deformation at interfaces of different-modulus media. After 2D tests of interface elements, an optimal type of the interface element was selected for the 3D modification implementation. The latter can improve reliability of geomechanical forecasts in mineral mining in complicated geological and geodynamic conditions. From the test data on modification of interface elements, the optimal interface element is assumed to be the six-node interface element proposed by V. Kalyakin and Jianchao Li. The six-node interface element is introduced in the model of a tunnel with simulation of an unloading line at the boundary. The adequate results on adjacent rock deformation are obtained. The 3D interface element modification reveals its peculiarities and limitations as regards introduction in finite element models of mineral deposits and enclosing rock mass. The ways of solving these problems are proposed.