During freezing periods, nutrients (carbon and organic matter, etc.) are enriched in the water and sediment of lakes in cold-arid regions, leading to potential algal bloom outbreaks and other health risks to the ecosystem. Particularly, dissolved organic matter (DOM) is a critical component of the nutrients and plays an important role in the global carbon cycle. However, the mechanisms of DOM transfer between ice and water remain unclear. This study analyzed the influence of microbial community on DOM composition using 16 s RNA, 3DEEM, and FT-ICR MS in Daihai Lake and Wuliangsuhai Lake in the Yellow River Basin, China. According to the spectral analysis, the content of endogenous organic matter, such as humus, accounted for 40% of the total DOM in water, while the content of tryptophan and tyrosine accounted for 80% of the total DOM in ice. The results of mass spectrometry showed that lignin was the main component, and the content of organic matter in the ice was less than that in the water. Molecular structures of seven DOM coexisting in the lake ice and water were elucidated with adapted Kendrick-analogous network visualization, which clearly illustrates that long-chain DOM molecules are derived from small molecules, while other heteroatoms are complexed with the side groups. The positive correlations between CHO, CHNO, CHOS, CHOS and Actinomyces indicate that DOM actively interacted with the microbial community. 44% of CHO compounds have the same molecular formula in water, the content of CHOS in the water of the two lakes was closed to 7% higher than that in the ice. Meanwhile, DOM dynamically migrate between ice and water via interstitial water because of the solubility changes under microbial transformation, which has been proved by the decrease in the contents of the humus and tryptophan-like substances in the ice from the bottom to the surface and lower contents of carbohydrate and unsaturated aromatic hydrocarbon in the water than the ice. This study helps to predict the composition and structure of DOM during the migration in lakes and provides a scientific basis for environmental remediation with high concentration of carbon.