Chlorophyll is the important index to estimate the phytoplankton biomass. In order to research phytoplankton biomass and eutrophication condition of water, the spectroscopy method has been used usually now. A large number of spectrum experiments also need to be taken in the laboratory. In this article, the gray and the white diffuse reference scale are respectively used to measure the character reflectance spectrum of the chlorophyll-containing water. Then we analyze the differences of the data quality between these two ways. The result shows that, when measuring the water object which has low reflectance in the laboratory, using the white scale will cause a big data noise and the data quality will be poor. But when using the gray scale to take the experiment, the data noise will be small and the data quality will be good enough to find the character reflectance spectrum.