PtAl coated Ni-based single crystal (SC) superalloys are widely used in the aerospace industry and land-based power generation applications. Interdiffusion between the coating and the underlying substrate inevitably occurs during thermal exposure at high temperatures, which causes considerable deterioration of mechanical properties in the alloy substrate. In order to reduce weight and film cooling, the thickness of single crystal superalloy blades is getting thinner and thinner. However, to the knowledge of the authors, the interface evolution mechanism of PtAl coated thin-walled single crystal superalloy and the effect of the substrate thickness have rarely been reported. In this paper, the mechanism of microstructural evolution of PtAl coated thin-walled Ni-based single crystal superalloy with different thicknesses has been studied. PtAl coatings are prepared on a third generation nickel-based single crystal superalloy DD9 with different thicknesses (0.5 mm, 1.0 mm and 2.0 mm) by electroplating Pt and high temperature and low activity vapor aluminizing. The thickness of the electroplating Pt layer is about 5 μm, and the final thickness of PtAl coating is about 40 μm. The inter-diffusion of elements and the microstructural evolution of the PtAl coated samples with different thicknesses have been studied by XRD, SEM and EDS. The inter-diffusion zone (IDZ) increases rapidly after isothermal oxidation for 100 h. After isothermal oxidation for 500 h, the IDZ thickness of three samples are about 25 μm and keep basically unchanged. However, only the sample with 0.5 mm thickness shows topological close packed (TCP) phase depleted zone in IDZ after isothermal oxidation for 1 000 h. Secondary reaction zone (SRZ) with needle-like and granular TCP phases forms below the IDZ in all the samples. After isothermal oxidation for 100 h, the thickness of SRZ of the three samples are equivalent. Still, after isothermal oxidation for 500 h and 1 000 h, the SRZ thickness of the sample with 0.5 mm thickness is significantly smaller than that of other two samples. Although the obvious inner diffusion of Al from the coating to the substrate has been found, the content of Al in the SRZ is basically unchanged due to that most inwardly diffused Al is absorbed in the IDZ. Microstructural analysis suggests that the enrichment of Ta rather than Al near the interface mainly leads to the formation of SRZ. The difference in diffusion of refractory elements such as W, Re and Ta at the interface is the key factor that causes different morphology/thickness of IDZ and SRZ in the three samples. The coated sample with the minimum thickness is easier to homogenize, and less interdiffusion of refractory elements such as W, Re occurs when the isothermal oxidation time is extended to 500 h, which leads to the minimum SRZ thickness of the sample with 0.5 mm thickness. The inward diffusion of Ta from the substrate to the IDZ has been reduced when the isothermal oxidation time is extended. However, the outward diffusion of Ta from the IDZ to the coating continues due to oxidation consumption. Therefore, the content of Ta has been reduced in the IDZ, resulting in the TCP phase depleted zone in the sample with 0.5 mm thickness.