In order to optimize the fluorescence detection capillary electrophoresis system and improve the detection sensitivity, the signal noise characters were studied when separating 100~1 000 base pair deoxyribonucleic acid ladder under direct current electric field in hydroxyethyl cellulose solutions. The dependence of signal noise on separation electric field intensity, polymer concentration, hydroxyethyl cellulose molecular weight, the effective length and the capillary shape were investigated. Experiment result shows that optimum parameters can be obtained under best signal noise ratio, which are the separation electric field strength of 500~600 V/cm, hydroxyethyl cellulose concentration of 0.6%~0.7%、hydroxyethyl cellulose molecular weight of 250, round inner diameter of 50 μm and effective capillary length of 8 cm.