This paper introduces a kind of new homemade and low cost multi-channel nucleic acid pyrosequence detector for at least ninety-six channels and presents the detail of related software and hardware development. We construct a kind of automatic instrument to fulfill the pyrosequencing processes. First we select the X-86 personal computer as host computer, the AT89C51 micro-controller as slave computer, the PMT (photoelectric multiply tube) as photoelectric transformation equipment, and the HY-6022 as data sampling device; Second we use the Visual C++ 6.0 as coding tools to design the measure and control system based on Windows 2000 operating system; Third we sample the fluorescent signal in all of the cuvettes during the reaction between nucleic acid and reagent; Last we analyze these data to realize the function of the multi-channel nucleic acid detection. In this paper the whole instrument design and key parts design are both introduced such as the liquid injection process and related structure design, the communication module between the host personal computer and the MCS51, the high sensitivity multi-channel detector (at least 96 channels, the sensitivity is 2.45×10-9w) etc. The result of the instrument for two channels data processing is also reported in this paper.