We first reported a strategy for promoting fluorescent aggregation nanocluster of cystine molecule by heating in constant temperature bath and this performance could be used for detecting quantity of cystine. The effects of pH value, reaction time and temperature on the system were investigated and the mechanism of photoluminescence was discussed. The results suggested that the non-fluorescent molecule was assembled to form Fluorescent Aggregated Nanoclusters (FANC) by heating the pH 9.0 0.01 mol·L-1 cystine solution at 90 ℃ for 12 hours, and its aqueous solution showed a maximum absorption at 410 nm and a fluorescence emission at 508 nm. The fluorescence performance and structure of FANC were characterized by fluorescence spectroscopy (FL), transmission electron microscopy (TEM) and mass spectrometry (MS). The average fluorescence lifetime of the FANC aqueous system is 6.028 ns and the fluorescence quantum yield is 8.48%. Moreover, FANC has stable photobleaching, acid-base stability and spectral dependence in aqueous solution. TEM images showed that the fluorescent FANC has a size of 12.5 nm, however, DLS size distribution of FANC is about 150 nm, suggesting that the aggregates of cystine has a hydrophilic surface. Zeta potential result is -57 mV, demonstrating that the nanocluster has a negative charge. Additionally, the results of mass spectrometry showed that there are molecular fragments formed by the intermolecular dehydration of cystine in the system. Therefore, we can further speculate that FANC is an inner molecular aggregation of cystine to form the supramolecular vesicles in the aqueous solution environment due to intermolecular forces. The relative fluorescence peak intensity of FANC and the concentration of cystine showed a good linear relationship in a certain range of 1.0×10-5～6.0×10-4 mol·L-1, and the detection limit of 4.559×10-9 mol·L-1(3S0/K). The proposed method was applied to the quantitative analysis of cystine tablet. The results were consistent with the titration result of Chinese Pharmacopoeia. Compared with other detection methods, this new method has the advantages of simple operation, low detection limit and high precision.