Lakes are hot spots for methane (CH₄) emissions and particulate organic carbon (POC) production, which describes the methane paradox phenomenon. However, the current understanding of the source of POC and its effect on CH₄ emissions during eutrophication remains unclear. In this study, 18 shallow lakes in different trophic states were selected to investigate the POC source and its contribution to CH₄ production, particularly to reveal the underlying mechanisms of the methane paradox. The carbon isotopic analysis showed that the δ¹³C_poc ranged from −30.28 ‰ to −21.14 ‰, indicating that cyanobacteria-derived carbon is an important source of POC. The overlying water was aerobic but contained high concentrations of dissolved CH₄. Particularly, in hyper-eutrophic lakes, such as Lakes Taihu, Chaohu, and Dianshan, the dissolved CH₄ concentrations were 2.11, 1.01, and 2.44 μmol/L, while the dissolved oxygen concentrations were 3.11, 2.92, and 3.17 mg/L, respectively. The intensified eutrophication increased the POC concentration, concomitantly promoting the dissolved CH₄ concentration and the CH₄ flux. These correlations revealed the role of POC in CH₄ production and emission fluxes, particularly as a possible cause of the methane paradox, which is crucial for accurately evaluating the carbon budget and balance in shallow freshwater lakes.