Transparent layers are critical for enhancing optical contrast of graphene on a substrate. However, once the substrate is fully covered by large-area graphene, there are no accurate transparent layer and reference for optical contrast calculations. The thickness uncertainty of the transparent layer reduces the analytical accuracy of graphene. Thus, in this Letter, we propose a reference-aided differential reflection (DR) method with a dual-light path. The accurate thickness of the transparent layer is obtained by improving the DR spectrum sensitivity using a designable reference. Hence, the analytical accuracy of graphene thickness is guaranteed. To demonstrate this concept, a centimeter-scale chemical-vapor-deposition-synthesized graphene was measured on a SiO2/Si substrate. The thickness of underlying SiO2 was first identified with the 1 nm resolution by the DR spectrum. Then, the thickness distribution of graphene was directly deduced from a DR map with submonolayer resolution at a preferred wavelength. The results were also confirmed by ellipsometry and atomic force microscopy. As a result, this new method provides an extra degree of freedom for the DR method to accurately measure the thickness of large-area two-dimensional materials.