Chromatic confocal microscopy is a widely used method to measure the thickness of transparent specimens. In conventional configurations, both the illumination and imaging axes are perpendicular to the test specimen. The reflection will be very weak when measuring high-transparency specimens. In order to overcome this limitation, a special chromatic confocal measuring system was developed based on inclined illumination. This design was able to significantly improve the signal-to-noise ratio. Compared with conventional designs, the proposed system was also featured by its biaxial optical scheme, instead of a coaxial one. This biaxial design improved the flexibility of the system and also increased the energy efficiency by avoiding light beam splitting. Based on this design, a prototype was built by the authors’ team. In this paper, the theoretical model of this specially designed chromatic confocal system is analyzed, and the calculating formula for the thickness of transparent specimen is provided accordingly. In order to verify its measurement performance, two experimental methodology and results are presented. The experimental results show that the repeatability is better than 0.54 μm, and the axial measurement accuracy of the system could reach the micron level.