Eutrophication induced by human activities may has a critical impact on the carbon cycle of Lake Taihu. Assisted by the technique of Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS), we investigated the molecular characteristics of dissolved organic matter in Meiliang Bay of Lake Taihu over the algal blooming-disappearance cycle at 2017-2018 to better understand the influence of algae blooming to the dissolved organic matter pool. The results show that during the algal-blooming period, the massively increasing productivity from algae have changed the amount and the molecular characteristics of dissolved organic matter in water from Lake Taihu. Basically, the concentration of dissolved organic carbon as well as the proportion of the relatively labile components (CHO-compounds, aliphatic compounds, and low-molecular-mass compounds with higher H/C and O/C values) increased during the algal-blooming period. While in the algal-disappearance period, due to both the low input of algal biomass and the continuous degradative progress of dissolved organic matter in the water column, the concentration of dissolved organic carbon decreased. Synchronously, the proportion of the relatively refractory components (CHOS-compounds, CHONS-compounds, CRAM compounds, high-molecular-mass compounds, and low-molecular-mass compounds with lower H/C and O/C values) increased. The dynamics of the molecular characteristics of dissolved organic matter in Meiliang Bay of Lake Taihu indeed propose the critical impact of eutrophication on the regional carbon cycle, asking for further research.