In this paper, a new method for measuring the thickness of transparent specimens using chromatic confocal microscopy (CCM) is presented. The conventional CCM thickness measurement model relies on capturing the focal points on the upper and lower surfaces of a transparent specimen. This model has strict specimen placement tolerance and a limited measurement range. In order to overcome these limitations, a new thickness measurement model was developed by adding an auxiliary reflector below the specimen. The thickness of the specimen can be determined by comparing the wavelengths of light focused on the auxiliary reflector before and after placing the measurement specimen. Theoretical analysis and simulation showed that the proposed method has twice the measurement range of the conventional model. In order to verify the proposed CCM measurement model, a laboratory thickness measurement system was developed by the authors’ team. A commercial laser scanning confocal microscope (Carl Zeiss LSM780) was used as the reference system. A set of quartz glasses was measured using both the proposed system and the reference system. Experimental comparison showed that the proposed method was able to achieve a measurement accuracy of 0.25 μm. In addition, repeated measurements conducted at different heights showed negligible variation. Thus, it can be concluded that the specimen placement tolerance was improved significantly compared with the conventional model.