This study investigates a Nickel-based single crystal (SX) superalloy with femtosecond laser-drilled film-cooling holes (FCHs) under varying temperatures (room temperature, 850 °C, and 980 °C), employing a novel framework for predicting fatigue life based on initial manufacturing damage quantification. For all tested anisotropic SX superalloy specimens (including smooth and FCH specimens), the initial damage state is characterized as an equivalent initial flaw size (EIFS), and an EIFS calculation model considering stress concentration is established. Subsequently, the fatigue crack paths and microstructural characteristics of the FCH specimens at different temperatures are analyzed, elucidating crack initiation mechanisms and propagation patterns. A novel incremental plasticity J-integral driving force for fatigue crack propagation is introduced. By incorporating the closure effect of small crack propagation and employing Markov Chain Monte Carlo simulations for determining crack growth rate probabilities, a more accurate expression for the crack growth rate in relation to ΔJfat − ΔJth is derived. This expression comprehensively captures crack patterns on crystallographic planes and Type I mixed mode behavior. Finally, the total fatigue life of the FCH structures, featuring a threefold dispersion zone in both room and high-temperature environments, is predicted through experimental observations and description of crack growth rates. The predicted outcomes significantly outperform those of the conventional life prediction models reliant on crystal plasticity theory.