The present invention discloses a biochip detection system for detecting a biochip labeled with multiple fluorophores. The biochip detection system comprises a broadband light source for generating a light beam, a stand for supporting the biochip, a light integrator positioned between the broadband light source and the biochip, a lens set for adjusting the cross-sectional area of the light beam, a first filter module positioned on the optical path of the light beam, a detector, e.g., CCD camera, photodiode array, for detecting a fluorescence beam emitted from the biochip, and a second filter module positioned on the optical path of the fluorescence beam. The light integrator can be a light tunnel, a lens array or a holographic diffuser for uniforming the intensity distribution of the light beam and changing the cross-sectional shape of the light beam into a rectangle.