The conventional parameters such as COD and BOD only could represent information about total organic content. Fluorescence spectrum can display organic composition and it is unique for each sample, so it is referred as “fluorescence fingerprint”. In the present study transformation of excitation-emission matrix of municipal wastewater with sewage as major components after aerobic treatment was investigated and then the zones of biodegradable and non-biodegradable organic matters were figured out: the fluorescence at excitation wavelength/emission wavelength of about 280/340 nm and 225/240 nm derived from biodegradable organics and those of the zone of excitation wavelength above 300 nm and the zone of excitation wavelength below 300 nm and emission wavelength above 400 nm were mainly related with non-biodegradable organics. The above-mentioned results indicated that fluorescence fingerprint could be used to evaluate the performance and instruct design and operation of aerobic systems.