This research has successfully developed a multiple fluorescence detection method for high throughput capillary electrophoresis detection using a digitally-modulated light source and a spectrum detection system. A commercial available LCD (liquid crystal device) projector is adoped to replace the spacially-filttered light source (Hg lamp) in a conventional fluorescence microscopy. The LCD projector can be digitally controlled by a computer to create the three primary colors of RGB (red, green, and blue) for fluorescence excitation in the analytes. The emitted light from the fluorescent samples is then collected using a UV-VIS-NIR spectrometer through a ultimode fiber. Delicate optical components, such as filter wheel or acousto-optic filtering system, for filtering different excitation light sources can be excluded with this simple and novel approach. In addition, the desired wavelength for the excitation light can be selected quickly and smoothly without vibration problems come with the mechanical optical components. Three fluorescent dyes (Atto 647N, Rhodamine B, Fluorescein) with different excitation and emission wavelength has been used to demonstrate the proposed digitally-modulated light source system for high throughput CE system. The optimal operation conditions for obtaining best detection signal-to-noise ratio for different fluorescence dyes are firstly determined. In addition, the current study proposes a mixed-color light (visually in purple) composed of two specific primary lights (red and blue) to simultaneously excite a mixed sample composed of two fluorescent dyes (Atto 647N and FITC). Separation and detection of the mixed fluoresce samples using a single excitation illumination using the proposed digital-modulated CE system is successfully demonstrated. Finally, a single-strand DNA biosample is used to confirmed the proposed system is feasible of adopting in the bio-analytical applications. The technique proposed in this study has shown its potential to be a high throughput CE detection system.