To realize rapid quantitative detection of bacteria found in drinking water, a high-throughput quantitative detection system based on flow cytometry was established. The systems signal acquisition system, absolute counting method, and comprehensive performance for bacterial detection were investigated and evaluated. Firstly, according to the fluorescent dyes of typical bacteria found in drinking water and their fluorescence excitation spectra, the working principle and hardware platform of the flow cytometer for rapid bacterial detection were established. Secondly, the signal-to-noise ratio of the signal acquisition system was evaluated by simplifying the calculation model for signal strength of bacterial fluorescence. Next, a calculation method based on the flow sensor method was established for absolute counting. Finally, a series of statistically analyzed control experiments were performed with the self-developed instrument alongside BD LSR Fortessa with absolute reference according to the reference microsphere method. The performance of the self-developed instrument for the detection of bacteria in drinking water was comprehensively tested and evaluated. The experimental results indicated the followings: for a 4 MHz wideband fluorescent signal, the signal-to-noise ratio of the signal acquisition system can reach 86 dB; for microspheres in a certain concentration range, the cv value of the system test results is less than 2%, the correlation coefficient with the test results of the BD instrument is as high as 0.999 6, the linearity of the equivalent dilution microsphere test is up to 0.999 8, and the lowest detectable bacterial concentration is 102 particles/mL; for E.coli and S.aureus bacteria, the cv value of the test results of the system is less than 7%, the correlation coefficient with the test results of the BD instrument exceeds 0.995 9, and the relative deviation is within 4%. The instrument is capable of rapid quantitative detection of bacteria with a high-precision, providing a reference for the development of rapid detection instruments for typical bacteria found in drinking water.