The discrete element numerical method has been usually used for some parameter sensitivity analysis of geo-materials in the compression test and the Brazilian splitting test. However, there have been limited studies systematically focusing on mesoscopic influencing factors and 3D fracture process in mode I fracture toughness tests. The 2D discrete element methods cannot reflect the real mechanical behavior of a 3D model. Therefore, a three-dimensional flat joint model (FJM3D) is used in this paper to investigate the effects of microstructure parameters and bond mesoscopic parameters on mode I fracture toughness tests with different notch shapes. The microstructure parameters include the square root of average particle radius ( ), model resolution ( ), and maximum/minimum particle diameter ( ). Bond meso-parameters include average coordination number (CN), slit element fraction ( ), bond tensile strength ( ), bond cohesion ( ), friction coefficient ( ) and friction angle ( ). Results of parameter sensitivity analysis show that the mode I fracture toughness ( ) is positively correlated with , CN, and , and negatively correlated with and . There are no obvious linear relationships between and , , , . In addition, suitable ranges of and are recommended to obtain an appropriate mode I fracture toughness with a low level of variation. Based on the results of parameter sensitivity analysis, the mechanical behaviors of the Kowloon granite with notched semi-circular bend (SCB) and cracked chevron notched semi-circular bend (CCNSCB) specimens are calibrated. The failure process of mode I fracture toughness tests with different notch shapes indicates that the pre-peak and post-peak behaviors of the SCB test is more consistent with the laboratory test.