Nanoindentation is generally used to measure the hardness or Young’s modulus of thin films. However, when the hardness or Young’s modulus is measured on the ultrathin layer, it cannot sometimes obtain exact results due to some influential factors such as wear of indentation tip, surface roughness, or substrate effect. We focused on the elastic modulus measurement method of ultrathin layers using the time-of-flight secondary ion mass spectroscopy (TOF-SIMS) with Ar gas cluster ion beam (GCIB). The dissociated ion yield defined as the intensity ratio (Ar₂⁺/(Ar₂⁺+Ar₃⁺) on the positive ion spectrum and impulsive stress were compared and correlated to be proportional to both on the reference materials. The Young’s moduli of the silicon oxide layer of 1.7 nm thickness on monocrystal silicon wafer and ultrathin diamond-like carbon (DLC) layer with approximately 3 nm thickness on magnetic disks were estimated using the dissociated ion yield measured using Ar-GCIB and correlation result. The Young’s modulus was measured at various depths using Ar-GCIB etching with a very slow etching speed. We confirmed a difference between the Young’s moduli of these ultrathin layers and those of under layers. From these results, it was seen that the elastic modulus measurement method using TOF-SIMS with Ar-GCIB is a powerful tool to compare the elastic modulus of ultra-thin layers and improve the accuracy of structural analysis simulations of ultra-thin film structures with nanometer order thickness, which was impossible with conventional methods.