This study examined the applicability of a prism-type simultaneous dual-color total internal reflection fluorescence microscopy (TIRFM) system for the simultaneous detection of nano biomolecules on nanoarray biochips at the single-molecule level. The dual-color TIRFM system with two individual laser beams and a high-sensitivity camera was used for the simultaneous dual-color detection of two different nano beads (i.e. 20nm yellow–green and crimson fluorescent FluoSpheres beads), and single-protein molecules labeled with different fluorescent dyes (i.e. actin from rabbit muscle conjugated with Alexa Fluor ® 488 and Alexa Fluor ® 633 goat anti-rabbit IgG) without a time-delay and the need to move the sample. When this system was applied to two different single-protein molecules labeled with different fluorescent dyes on the GPTS/CHI/GA-modified glass nanoarray chip, the full images of the biomolecules at the single-molecule level were obtained simultaneously in two different colors using a Dual-View™. The dual-color TIRFM system is quite suitable for the biological imaging at the single-molecule level on nanoarray biochips. This study provides a benchmark for directly monitoring the interactions and detecting the colocalization of two different nano biomolecules, and can be applied to the development of a nanoarray biochip at the single-molecule level.