Grain-based models (GBMs) are widely used to analyse the micromechanical characteristics of granite. However, the classical two-dimensional (2D)-GBM has some shortcomings: poor matching of mineral composition and grain size distribution to the rock, small number of intragranular microcracks, and inability to represent the three-dimensional (3D) structure of the grains. Therefore, we propose a new method to establish a 3D-GBM in the particle flow code (PFC). The PFC3D-GBM parameters are obtained by calibrating the experimental data, such as the elastic modulus, Poisson's ratio, tensile strength, compressive strength, Hoek-Brown (HB) strength criterion, and fracture characteristics. The fracture mode of granite is analysed on the basis of the experimental and simulation results. In addition, the fracture characteristics and microscopic fracture mechanisms of granite are analysed from the perspective of mineralogy. The results reveal that the mineral composition and the grain size distribution of PFC3D-GBM match well with those of the rock, and the model can simulate the macroscopic and microscopic fracture characteristics of granite. This provides an effective way to study the relationship between microscopic parameters and macroscopic behaviours in a 3D model.