A multiphoton excitaion microscope for simultaneously detecting differently colored fluorescence materials on biochips includes a multiphoton excitation source, objectives, and a plurality of detection channels. The biochip is hybridized and labeled with fluorescence materials for expressing hybridized biological signals. The multiphoton excitation source is focused to a light spot on the biochip to excite the fluorescence materials bound thereon. After that, the fluorescence emission at different wavelengths from the different fluorescent materials can be detected by the plural detection channels.