Scanning detection of biochip based on fluorescence labeling is introduced in the paper, the detection method can be divided into two category: one is confocal scanning detection method in which a photomultiplier tube is used as fluorescence sensor, the other is flood illumination of the entire biochip and uses CCD as fluorescence sensor. A novel method of fluorescence detection for biochips is presented, which uses a 532 nm laser and 635nm laser to excite the fluorescent dyes according the principle of laser confocal scanning. The fluorescence emitted from cy3 and cyo is detected using a photomultiplier tube (PMT) sequentially. One dimension scanning of the biochips is performed by a telecentric f-θ objective with a moving coil optical scanner, the other dimension is scanned by a stepping motor driving the precision guidance. The experiment results state that the resolution of the presented technology is 5 μm, the signal-to-noise ratio can reach 10s and the detection limit is 1 fluor/μm2, and the cross-talk phenomenon is eliminated completely.