A fluorescent microarray analyzer includes a light source for emitting a light beam, a light processing unit for focusing the light beam on the biochip and exciting fluorescent targets on the biochip to produce fluorescence, a focusing lens for focusing the fluorescence on a spectrophotometer, a spectrophotometer for detecting signal of the fluorescence, and an output device for selectively outputting/displaying the signal detected by the spectrophotometer. The resulting signal of the output device does not need to be converted into image data for analysis. For acquiring a more accurate result of detection of signal of fluorescence from the fluorescent targets, the photomultiplier tube of the conventional biochip scanner device is replaced with the spectrophotometer of fluorescent microarray analyzer of the present invention and the filter is removed. Without converting the signal into an image, no errors arise as what happened in process of converting an electrical signal into image data in the conventional biochip. Also, a real-time analysis of the signal proceeds while scanning samples on the biochip.