Flexible displays are lightweight, thin, flexible, and impact-resistant, making them a major trend in the display industry. However, their short lifespan is a significant challenge. Thus, improving process parameters and extending product life through advanced measurement technology is crucial. Therefore, this study proposes using tomography common optical path interferometry (TCOPI) to measure and analyze the tomography stress characteristics of multi-thin-film flexible substrates in the folding direction. For polyethylene terephthalate (PET) and polyimide (PI), three thicknesses of indium tin oxide (ITO) were coated on the PET, graphene/PET, and graphene/PI flexible film substrates, and an automatic sliding-folding test platform was used to fold each flexible film substrate. Moreover, this study used TCOPI to measure and analyze the change in residual stress and the sheet resistance of the samples before and after folding. Additionally, this study conducted inward and outward folding tests on graphene/PET/graphene and graphene/PI/graphene substrates to analyze tomographic stress and sheet resistance in the folding direction. After 11,000 folding tests, the graphene/PET/graphene sample exhibited smaller stress and sheet resistance change rates compared to the graphene/PI/graphene sample, as measured by TCOPI. Consequently, the graphene/PET/graphene sample demonstrated better resistance to folding stress in this batch manufacturing process. Specifically, for the graphene layer of the graphene/PET/graphene sample, the minimum absolute value of the stress change rate before and after folding reached 5%. At the same time, the minimum sheet resistance value change rate was 8%. Based on the tomography stress measurements, suggestions for fine-tuning process parameters are provided to improve the flexible film substrate’s folding endurance.