Abstract: The global warming caused by greenhouse gases emission has raised serious concerns. Recent studies found that the carbon dioxide (CO₂) and methane (CH₄) emissions from river ecosystem can partly offset the carbon sequestration by terrestrial ecosystem, leading to a rethink of the effects of river ecosystem on the global carbon balance and greenhouse gases emission inventory. As an important primary producer in urban river ecosystem, filamentous macroalgae can deeply affect the carbon cycle process of river system through changing the abiotic and biotic factors in the interface of water-sediment. This paper reviewed the effects of filamentous macroalgae on the CH₄ emission from urban river system from the aspects of 1) the effects of urbanization on the river ecosystem and its CH₄ emission flux, 2) the effects of filamentous macroalgae on the CH₄ generation and emission process in natural river systems, and 3) the effects of filamentous macroalgae on the primary productivity and CH₄ emission process in urban river systems. The current problems and future directions in related researches were discussed and prospected.