A novel multi-channel DNA fragment analysis system is presented，which is based on single PMT confocal fluorescence detection and optical scanning adopting an f-theta lens. Capillary electrophoresis experiments were executed in the system for DNA marker pBR322/Hae III. Signal was processed with wavelet denoising. The system’s limit of detection (dsDNA with the probe of Thiazole Orange, TO) was evaluated to be 1.1841×10-11mol/L. Its working noise is much lower compared with that based on mechanical scanning one, and the stability and detecting sensitivity is high. The system was expected to be applied to both capillary array and microchip electrophoresis detection based on laser-induced fluorescence.