The role of adaptation as an interdisciplinary phenomenon and the necessity of its evolvement in engineering sciences, including mining, is stated. The notion of “open pit transportation system adaptation” is defined. The research was aimed to justify the choice of a methodology for adapting transportation systems in open pit mines, as well as to demonstrate possibility of the transportation system behavior determination and forecasting. In accordance with the definition, the state of a transportation system in the course of adaptation is described. It is shown that the theory of transportation systems for open pits and the theoretical principles are the mainframe. The theory features flexibility, is continuously developed and upgraded, meets the recent methodological standards and can serve the basis of structural and parametric adaptation. The case-studies of the efficient problem solution in mining using the universal simulation model of transportation system functioning in open pit mines developed at the Institute of Mining, Ural Branch RAS are presented. The scope of the applied research embraced: validation of parameters for loading-and-rehandling points in the dump truck- belt-rail transport flowcharts; determination of carrying capacity of rail tracks in open pits; justification of transportation system parameters for open pit mines based on the interactive modeling. The theoretical methodology framework for transportation system adaptation in open pit mines is presented, which is the joint application of the theory of transportation systems in deep open pit mines in structural and structural-and-parametric adaptation and the universal interactive simulation model of transportation system functioning in open pits in parametric adaptation.