Dissolved organic matter (DOM) played important roles in aquatic systems, which could act as a food source for microbes, affect the availability of nutrients, trace metal and the air-sea CO₂ flux. Natural DOM is a complex mixture and composed of tens of thousands of molecules, which includes amino acid, lipids, lignin etc. The cycling of different DOM, on one hand, was affected by the environment, e.g., temperature, availability of nutrients and microbial community. On the other hand, depends on its intrinsic property, e.g., aliphatic organic matter is more easily to be biodegraded, while aromatics are relatively resistant to biodegradation, but prone to photo-bleaching. Generally, the composition of DOM can be affected by the sources. For estuarine areas that are close to the inland, it usually contained more terrestrial DOM (tDOM), while for open oceans the tDOM may have been partially degraded and the DOM can be more modified by the on-site biological activities. Under the influence of global warming, both the temperature and the molecular composition of DOM will change, and so will affected the degradation of DOM. Besides, the variation of the biodegradation of DOM under the warming effect can be varied with sources. Here we took Jiulong River Estuary (JRE) and Xiamen Bay (XMB) as the two different study sites, took the dissolved organic carbon (DOC), UV-vis spectrum as the study methods, and regulate the degradation temperature to study the responses of the biodegradation of various DOM components from different sources to temperature variation. The results show that although DOC concentration is decreasing with the incubation time in both JRE and XMB, the temperature increasing causes the increasing utilization of DOC in JRE while causes no significant change in XMB. Under the action of biodegradation, the chromophoric dissolved organic matter (CDOM) prone to be transformed in JRE in the early incubation stage, and then to be utilized in the late stage, while in XMB CDOM decreased during the entire period. Meanwhile, the temperature increasing inhibited the transformation and utilization of CDOM in JRE, while promoted the utilization of CDOM in XMB. In addition, the temperature can also affect the changes in molecular weight and aromaticity during biodegradation. Our results indicate that the biodegradation of different DOM components is affected by both sources and temperature. We predicted that with the increasing of temperature, a larger proportion of DOM could be biodegraded and meantime, release more bio-refractory DOM.