Fluorescent digital image correlation (DIC) is becoming popular for measuring 3D profiles and deformations in external surfaces. However, the simultaneous monitoring of interior layers is highly challenging due to the penetrability and refraction of light using monochromatic fluorescence. We propose a color fluorescent speckle pattern (CFSP) method for measuring the internal displacement of transparent objects based on multispectral stereo-DIC and refractive index correction. During sample fabrication, fluorescent speckle patterns exciting different colors are fabricated on both the surface and interior layers of objects. A virtual color stereo-DIC system is utilized to capture the CFSP on the surface and interior layers simultaneously from two different perspectives. Different color channels are practically equivalent to synchronized monochrome vision systems, having separate CFSP in external and internal measurements. In multispectral stereo-DIC calculation, the external surface is initially reconstructed through one channel of the system even if the surface is non-planar. Based on Snell's law and the CFSP method, the internal layer is then reconstructed and corrected by establishing the geometry of the refractive stereo-DIC through another channel. The relative error of the thickness between two planar layers was proved to decrease from 33.4% to 0.7% after refractive index correction. Further experimental results validate the efficacy of this method for correcting the profile of the non-planar arc profile and determining the internal deformations of disc materials.