The composition of natural organic matter(NOM)in two different shallow lakes(Taihu Lake and Hongze Lake)was characterized by synchronous fluorescence spectroscopy. At the same time, the binding properties of NOM with Cu²⁺and Cd²⁺ were studied by fluorescence quenching titration test. The results show there are significant differences in the proportion of protein-like and humus-like components in NOM between the two lakes. The NOM of Taihu Lake is mainly composed of protein-like and humus-like substances, while that of Hongze Lake is mainly humus-like substances. There were significant differences in binding sites and binding capacity of NOM with Cu²⁺ and Cd²⁺ between Taihu Lake and Hongze Lake. The binding sites of humus-like substances in NOM were significantly more than that of protein-like substances. The binding ability of proteins to Cu²⁺ in NOM of Gonghu Bay and Meiliang Bay of Taihu Lake and the binding ability of proteins to Cd²⁺ in NOM of Meiliang Bay are stronger than humus-like substances, but the binding ability of proteins to Cd²⁺ in NOM of Gonghu Bay is weaker than humus-like substances. The binding ability of proteins to Cu²⁺ and Cd²⁺ in NOM of Hongze Lake was stronger than that of humus-like substances, while that of heavy metals Cu²⁺ and Cd²⁺ in Taihu Lake was significantly higher than that of Hongze Lake.