The invention provides a novel optical system for use in a microarray scanner, comprising an aperture-containing reflecting mirror comprising an aperture and a reflecting surface. The aperture of the aperture-containing reflecting mirror allows an excitation light to pass through, and the reflecting surface of the aperture-containing reflecting mirror allows emission light from a microarray to be reflected. The optical system may also comprises various other components such as laser generators, beam splitter, reflecting mirrors, excitation and emission light filters, excitation and emission objective lens, pinhole, and detector. The optical system described herein has high efficiency, high sensitivity, low background noise, structurally simple, and high versatility.