A study on the role of the irregular geometry of the α-Al2O3 film during the creep rupture test was conducted on samples of DD6 Ni-based single-crystal superalloy at 980 °C/250 MPa. This study involved experimental and finite element analyses of creep-oxidation specimens. The experimental results showed that the creep rupture life of the 0.67 mm-thin samples was shorter than that of the 0.81 and 1.12 mm specimens. Microscopic examination of the oxidation-affected zones showed that the morphology of the inner α-Al2O3 layer of a 0.67 mm-thin sample was discontinuous and incomplete, and the sample (1.12 mm thick) included a continuous and complete α-Al2O3 film. Hence, the influence of different morphologies of the α-Al2O3 layer on the stress distribution was studied numerically using the ABAQUS software. The finite element modeling results showed that the maximum stress was concentrated in the blocks of a discontinuous α-Al2O3 layer, which increased the diffusion of ions and metal cations. As a result, excessive growth of the oxidation-affected zone of the thin samples and the formation of AlN particles in high density occurred. It also contributed to an increase in the surface crack growth rate in the thin wall sample, which reaches the critical value of crack length in a shorter time than thick ones. Microstructure-based modeling has provided further insight into the role of the α-Al2O3 layer morphology in the deterioration of the mechanical properties of thin creep specimens.