It has been known that the absorption spectra of aqueous organic dye solutions tends to deviate from the Lambert-Beer law depending on solution conditions, which is considered to be mainly due to the dye aggregation caused by the intermolecular interaction among dyes. In this study, the visible spectra regarding two types of acid dyes in an aqueous solution, as well as the levelling type and milling type of acid dyes, were measured under different solution conditions such as changes of dye concentration and temperature. The non-negative matrix factorization (NNMF) method was adopted for the spectrum analysis. With the NNMF algorithm, several types of spectra caused by the dye aggregation could be measured and quantitative analysis for the dye aggregation was possible. When the concentration regarding the dye or dye solution temperature was changed, the two types of dye showed quite different aggregation behaviors which can be discussed with the hydrophobic property of the dyes.