As weak structural planes are difficult to be simulated reasonably in large underground chamber, “element reconstruction and node separation” was introduced, and the new simulation methodology of discontinuous weak structural planes was proposed in this study. The proposed methodology was used in the actual numerical model of underground powerhouse to simulate the discontinuous weak structural planes. The reconstructed model was then imported into calculation program, and the result was compared with the prediction by conventional continuous finite element model. The comparison shows that the reconstructed model can be used in the numerical calculation, and the discontinuity feature is presented near the discontinuous structural planes. Moreover, the rules in the calculation results are consistent with the general rules, which can describe the actual occurrence mode of the structural planes. Therefore, the simulation methodology of discontinuous weak structural planes achieves the transformation into the discontinuity of the structural planes, and it provides a new way for the simulation of complex geological discontinuous weak structural planes in large underground chamber.