An apparatus and method for simultaneously measuring, in an immersion microchannel environment, the characteristics of molecular junctions such as a low-molecular-weight biomaterial and the like and the refractive index of a buffer solution by using ellipsometry. Specifically, disclosed is an apparatus for simultaneously measuring, with high sensitivity, the change in refractive index of a buffer solution and the junction dynamic characteristics of a biomaterial by allowing polarized incident light to be received at a biomaterial adsorption layer, which is formed on a substrate such as a semiconductor and the like, so as to meet an anti-reflection condition of a P-wave by using a prism structure and a microchannel; and a measurement method using the same.