Freshwater aquatic ecosystem is an important source of greenhouse gases emission in the atmosphere. There is little research on greenhouse gases in urban artery-urban rivers (especially the channels with persistent high algae input). The discharge of high algae from Meiliang Bay of Lake Taihu into Liangxi River is a typical channel of high algae input, with a monthly averaged algae density of 3.6×10⁷ cells/L and a daily averaged algae density of 1.2×10⁸ cells/L in summer. In this paper, the fluxes of methane and carbon dioxide in Liangxi River were measured by static chamber method, and their characteristics and influencing factors were analyzed. The results show that on the spatial scale, the average methane flux is 4.63 μmol/(m²·s), and the average carbon dioxide flux is 98.87 μmol/(m²·s). Methane was released at all sections, and carbon dioxide was released at all points except the absorption state at Meiliang Bay pumping station. The diurnal observation of greenhouse gas flux at Hongqiao site shows that the peak value of methane flux appears in the evening, and the peak value of carbon dioxide flux appears around noon, and the diurnal variation is not obvious. The main factors influencing the beam river methane flux variation were river flow velocity, dissolved oxygen and suspended solids contents, Redox potential and pH value, hydrodynamic conditions and cyanobacteria packing density become the key factors affecting greenhouse gas emissions. The Liangxi River, as a typical algal input channel, exhibited much higher greenhouse gas emissions above the world average (carbon dioxide emission is 7.65 μmol/(m²·s), methane emission is 0.1 μmol/(m²·s)). Therefore, the study of greenhouse gas emission mechanism from persistent high algae input channels is of important theoretical support for accurate assessment of global river carbon emissions.