Based on the needs of rapid on-line monitoring of bacteria microorganism in water, a multi-wavelength transmission spectrum measurement system was set up. Ultraviolet transmission spectra of potassium dichromate standard solution and visible transmission spectra of neutral filter were measured by the experiment system, which were then compared with the transmission spectra measured by ultraviolet and visible spectrophotometer to validate the accuracy of the transmission spectra measured by the experiment system. Staphylococcus aureus which commonly existed in water was studied in this paper. Moreover, small angle transmission spectra of staphylococcus aureus were measured over a broad range of transmission wavelength (220~900 nm) by the experiment system. The results confirmed the accuracy and rapidity of the experiment system measuring the transmission spectra of bacteria microorganism. The transmission spectra of the potassium dichromate standard solution or neutral filter measured by the experiment system was strongly correlated with the transmission spectra measured by Ultraviolet and visible spectrophotometer, and their linear fitting coefficients were 0.999 7 and 0.999 5 (R2=0.999 7 and R2=0.999 5). The errors of optical densities measured by the experiment system were less than 5.00% and 4.58%, which showed that spectral consistency was better and ultraviolet and visible transmission spectra of standard samples measured by the experiment system had a high accuracy. The correlation coefficient of transmission spectra of the staphylococcus aureus measured by the experiment system after calibration fitted with that of ultraviolet and visible spectrophotometer is 0.999 97. As well, the error was less than 0.74% between the experimental system and ultraviolet and visible spectrophotometer. In addition, single measurement time of the average transmission spectrum measured by the system was 15s, which was 30 times of the signal acquisition. It showes that the experimental system can quickly and accurately obtain the multi-wavelength transmission spectra of bacterial microbial in water with respect to ultraviolet-visible spectrophotometer. The transmission spectrum measured by the experimental system is not only highly accurate, but also shortens the spectrum measurement time, which provides a technical support for the rapid detection of bacterial microbial in water.