Microcystic aeruginosa was cultivated in laboratory condition with nature water for about 95 days. Three dimensional excitation-emission (3DEEM) fluorescence spectroscopy and synchronous scan fluorescence spectroscopy of the culture water at different growth stages were measured, simultaneously the chlorophyll-a and extracellular MC-LR concentration were analyzed. The results show that fluorescence signal A, signal X and signal C could be observed obviously from 3DEEM fluorescence spectroscopy and synchronous scan fluorescence spectroscopy, which represent protein-like substance, marine humic-like acid and fulvic-like substance respectively. All the three fluorescence signals intensity and MC-LR concentration were normalized by chlorophyll-a concentration. In the decline phase, the normalized fluorescence signals(A, X, C) and normalized MC-LR concentration show the same dynamic laws and good linear correlation. The maximum values appeared at the same time. Therefore, MC-LR concentration can be estimated by the feature fluorescence signal (A, X, C) and chlorophyll-a concentration. Comparing to 3DEEM fluorescence spectroscopy, synchronous scans fluorescence spectroscopy (Δλ=80 nm) is less time-consuming and can give out the entire feature fluorescence signal (A, X, C). It is suitable for real-time analysis of water fluorescent spectroscopy which can be used to rapidly estimate the MC-LR concentration.