Thermally induced pores (TIPs) are generally the source of fatigue crack initiation in the powder metallurgy (PM) Ni-based FGH96 superalloy. The effect of TIPs on fatigue crack initiation on the surface of the FGH96 superalloy was detected using scanning electron microscopy (SEM). The cause of fatigue crack deflection was studied using electron backscatter diffraction (EBSD) analysis. The results indicated that there are two states of TIPs including isolated TIPs and clustered TIPs located at the grain boundary. The investigation of crack initiation and propagation around TIPs was conducted in detail through the comprehensive integration of experimental findings and computational results. For cracks initiated by isolated TIPs, the maximum equivalent size and the ratio of the vertical–parallel axis to the loading direction of the TIPs reveal a linear relationship, and both of them determine crack initiation. Regarding clustered TIPs, the constituent pores of the clustered TIPs will compete to initiate cracks based on the experimental results, and the largest pore will be more likely to initiate cracking. Moreover, the results showed that fatigue crack propagation can be hindered by hard-orientation grains and twins with a low Schmid factor (SF). Large-angle crack deflection due to twins with a low SF can significantly increase crack length and resistance to crack propagation.