In rock materials, the intergranular structure is more affected by various external conditions than the transgranular structure, and then dominates the macroscopic mechanical properties of rocks. In this paper, an innovative three‐dimensional grain‐based model based on Particle Flow Code (PFC3D‐GBM) for reproducing granite crystalline structures was developed. Based on this model, the Brazilian splitting test was conducted to investigate the effects of intergranular contact (IC) bonding strength on the mechanical properties and micro‐cracking behavior of the granite. Additionally, in this paper, the force chains and the orientation distribution of the force chains are shown in the form of three‐dimensional rose diagrams. The results are compared to the numerical results obtained by an initial particle‐based model to demonstrate the superiority of the proposed PFC3D‐GBM. The results indicate that the stress–strain curve of the sample in the Brazilian splitting test can be classified into four distinct stages: initial compaction, linear elasticity, damage, and splitting failure. ICs fracture at a higher rate than transgranular contacts (TCs) under static loading, as evidenced by experimental results of laboratory tests; during the entire loading process, all force chains uniformly distribute in all directions of a sample. As the external load increases, the number of total force chains decreases and the number of cracks increases. The main orientation of the high‐strength force chains is consistent with the external loading direction and is vertical with respect to the main orientation of the cracks. Furthermore, the number of high‐strength force chains increases with the level of external load. The sample's failure mechanism in the Brazilian splitting test is always a tensile failure, and this characteristic is unaffected by the modeling method or the IC bonding strength. Both the tensile strength and peak strain increase as the IC bonding strength increases. In this process, the number of total cracks in PFC3D‐GBM decreases, the proportion of transgranular cracks (Tcs) increases, and the proportion of intergranular cracks (Ics) decreases. The micro‐cracking behavior described above based on the PFC3D‐GBM can be explained more rationally. As the bonding strength of the IC increases, the particles involved in sample deformation are subjected to a greater stress concentration prior to the sample experiencing macro‐fracture, leading to an increase in the number of high‐strength force chains, which is the fundamental reason for the increase of the sample's tensile strength.