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Crack‐closure behaviour of rock materials is well‐known, while the three‐dimensional discrete element method (DEM) simulation of crack‐closure behaviour is still a challenge. Hence, a numerical method was proposed through the combination of notional surface method and flat‐joint model. The pre‐existing microcracks with finite width can be inserted into the three‐dimensional numerical sample through the present method. Since the two physical mechanisms, that is, closure of pre‐existing microcracks and fracture of flat‐joint bonds, are included in the simulations, various evolution trends of crack‐closure stage can be captured through the present method. Due to the high computational efficiency of flat‐joint model, the three‐dimensional DEM simulations of crack‐closure behaviour can be achieved. The results of parametric study show that the crack intensity determines the crack‐closure behaviour and the crack width significantly influences the evolution trend of crack‐closure stage. The simulated unconfined compressive strength (UCS) and tensile strength (TS) significantly decrease with the increase of crack intensity. The crack width significantly influences the deformation parameters, such as elastic modulus, Poisson's ratio and crack closure strain. A calibration procedure was proposed to ease the calibration of mechanical parameters and crack‐closure behaviour. Through the proposed numerical method and calibration procedure, the basic mechanical parameters and crack‐closure behaviour of sandstone were well matched. [ABSTRACT FROM AUTHOR]