The overgrowth of macrophytes has become serious due to increasing eutrophication in shallow lakes. The primary degradation processes of macrophytes litter, including photodegradation and biodegradation, induce considerable patchiness in the concentration and bioavailability of dissolved organic matter (DOM). In this study we investigated the composition evolution of DOM derived from emergent aquatic plant litter, Phragmites australis, in microbial degradation, photodegradation, and the combination of bio- and photo-degradation. Results revealed that the effects of photo- and biodegradation on the composition difference of macrophyte litter-derived DOM during short- and long-term degradation phase were different. Although large changes in DOM were observed after five days of incubation, the abundance and chemical composition were similar in the three treatments. However, more concentration of DOM was produced by combined photo- and biodegradation at the long-term degradation phase, and the composition of DOM showed less lignin-like formulae, as well as less condensed aromatic and aromatic compounds when compared to sole treatments. More reactive oxygen species (ROS) were found under the combined treatments, thus the contents of refractory components (condensed aromatic- and aromatic compound groups) were reduced. This study provide deeper insight into the fate of DOM and relevant biogeochemical processes in eutrophic lakes.