The principles of the microscopic fluorescence detection with frequency division multiplexing paralleling detection technology (FDMPD) is analysed. In the FDMPD system, the exciting laser beam is firstly divided into the multi-beams, and each beam is modulated with the individual carrying frequencies. The multi-beams exciting laser is focused on the surface of target cells to generate the multichannel fluorescent signals with corresponding carrying frequencies. Photomultiplier tube collected the fluorescent signals and transmitted the signal into the computer. Then individual channel fluorescent signal which varies with the time can be demodulated in a parallel and a high-resolution way. Employing 405 nm exciting laser sources, the two channel FDMPD system is constructed. The experiments explored micro-morphology of mouse nerve cells sample and demodulated the two channel fluorescence curves varying with the time. Furthermore, the basic parameters including the magnification, time resolution ability etc are analyzed, and the basic conditions to avoid the cross talk among multiply channels are also put forward.