Thermal barrier coatings (TBCs) are widely used to further extend the lifetime of turbine blades by protecting the blades from high temperature corrosion and oxidation. However, the mechanical behavior of turbine blades is obviously affected by the TBCs. In this study, microstructures evolution, damage mechanisms and life prediction of coated and uncoated nickel-based single crystal (NBSX) superalloy DD6 under isothermal fatigue load were investigated at 980 °C. The effects of TBCs on fatigue failure behavior and lifetime of DD6 were addressed. The results showed that the fatigue lifetime reduced with the increase of load. The effect of TBCs on the fatigue lifetime was related to the stress amplitude, as the effect was beneficial at high stress but almost negligible at low stress. Fracture morphologies showed that the cracks more likely initiated and propagated from basal defects for both coated and uncoated DD6, and the microstructure evolution also showed stress amplitude dependence. The crack density of uncoated DD6 increased first and then decreased with the increase of stress amplitude. However, the TBCs reduced the number of cracks that penetrate into the DD6 substrate, and the stress amplitude exerted a significant effect on crack propagation paths. In addition, the rafting behaviors of the DD6 substrate of coated and uncoated samples was compared, and results showed that TBCs could reduce the rafting degree of DD6. Finally, the fatigue lifetime of coated samples was predicted based on the modified Basquin model, and the prediction results fitted well with the experimental results.