In this study, microchip electrophoresis (MCE) was integrated with a two-dimensional photonic crystal (PhC) fabricated using nanoimprint lithography (NIL) for the detection of low-molecular-mass substances such as carbohydrates by determination of refractive index changes in solutions. The MCE-integrated PhC was fabricated using poly(dimethylsiloxane) (PDMS)-based micro-flow channels and NIL-based PhC. Different concentrations of sucrose solutions [0.5–20% (w/v), refractive index: 1.3337–1.3619] were introduced into a PDMS-based micro-flow channel by electro-osmotic flow (EOF), and the MCE-integrated PhC successfully detected fractional refractive index changes (0.0002) from the change in the optical characteristics of NIL-based PhC. Based on this detection principle, low-molecular-mass substances can be detected cost-effectively and easily without using a labeling procedure.