A defined refractive index is essential to measure the thickness of transparent materials with a chromatic confocal sensor (CCS). To overcome this limitation, a new measuring model is proposed by configuring a motor to drive the CCS for movement and placing a reflector behind the sample. This innovative approach enables the measurement of thickness and refractive index of transparent material synchronously through geometric calculations based on peak signals from different surfaces. Experimental results show that the model can achieve an average thickness measurement deviation of ±0.4µm and an average refractive index measurement deviation of ±0.005, making it highly suitable for industrial applications in thin film manufacturing sectors such as new energy vehicles, flexible displays, biomedicine, and more.