Abstract: The as-deposited coating–substrate microstructure has been identified to substantially influence the high-cycle fatigue (HCF) behavior of Ni-based single-crystal (SX) superalloys at 900°C, but the impact of degraded microstructure on the HCF behavior remains unclear. In this work, a PtAl-coated third-generation SX superalloy with sheet specimen was thermal-exposed at 1100°C with different durations and then subjected to HCF tests at 900°C. The influence of microstructural degradation on the HCF life and crack initiation were clarified by analyzing the development of microcracks and coating–substrate microstructure. Notably, the HCF life of the thermal-exposed coated alloy increased abnormally, which was attributed to the transformation of the fatigue crack initiation site from surface microcracks to internal micropores compared to the as-deposited coated alloy. Although the nucleation and growth of surface microcracks occurred along the grain boundaries in the coating and the interdiffusion zone (IDZ) for both the as-deposited and the thermal-exposed coated alloys, remarkable differences of the microcrack growth into the substrate adjacent to the IDZ were observed, changing the crack initiation site. Specifically, the surface microcracks grew into the substrate through the cracking of the non-protective oxide layers in the as-deposited coated alloy. In comparison, the hinderance of the surface microcracks growth was found in the thermal-exposed coated alloy, due to the formation of a protective Al₂O₃ layer within the microcrack and the γ′ rafting in the substrate close to the IDZ. This study will aid in improving the HCF life prediction model for the coated SX superalloys.