The invention discloses an optimal parameter method for determining electrophoresis detection based on capillary electrophoresis noise analysis. According to the invention, a capillary electrophoresis system is employed, 100-1000 base pair DNA is taken as a separating object, the noise characteristic of DNA separating by capillary electrophoresis in a hydroxyethyl cellulose solution under direct-current electric field, and an optimum system electrophoresis detection parameter is selected according to the noise characteristic of the system under different conditions. According to the invention, a capillary electrophoresis fluorescence signal is used for detecting noise source angle research in the system as well as analyzing the influence of the system detection performance by noise, and system optimal parameter is given. The main noise for influencing the detection performance is derived from noise caused from electrophoresis while unlatching. Noise with different separating electric field intensity, buffer solution concentration and molecular weight, and capillary effective type link can cause the electrophoresis noise fluctuation with different degrees. During an electrophoresis realization process, according to current condition, a apparatus parameter, a test article and a test reagent are selected in a reasonable mode, and optimum detection performance is realized.