Incremental hole drilling is a commonly employed semi-destructive method for measuring internal residual stresses. It involves calculating internal residual stresses through the measurement of strains. The conversion of strain to stress is achieved through calibration coefficients, the accuracy of which directly influences the precision of residual stress measurements. These calibration coefficients are predominantly determined through finite element simulations, which must consider the sample’s characteristics and realistic experimental conditions. While there has been extensive research on the influence of sample thickness, the impact of thickness under different experimental conditions remains unexplored, and the underlying physical mechanisms driving thickness effects remain ambiguous. This paper addresses this gap by employing finite element simulations to investigate the impact of thickness on calibration coefficients under three commonly utilized experimental conditions. Moreover, this research endeavors to elucidate the physical mechanisms that contribute to variations in these coefficients through energy analysis.