Dissolved organic matter (DOM) can be transported from mangrove wetlands to the ocean, as a key link in the global carbon cycle. The continuum between mangrove creeks and the ocean is a prime location for facilitating reactions between DOM and sunlight or microbes. Yet, little is known about the sources, transformation, and fate of DOM in the transport continuum at the critical land-to-sea zone. Here, water samples were collected in the estuary of southeastern China along mangrove creeks. We found that DOC concentrations ranged from 6.65 to 110.48 mg/L along the creek-to-estuary continuum. The high accumulation of DOC can be due to the high residence time of seawater and more sensitivity to environmental disturbance. 1.75 times higher DOC concentrations were showed in the lower area than the upper area of the transporting continuum. DOM materials in mangrove creeks were characterized by mostly labile, highly degradable proteins. Terrestrial index (TI) and marine-derived index (MI) were respectively used to described allochthonous and autochthonous characteristics of DOM. The DOM showed a high TI and low MI in the upper area and low TI and high MI in the lower area of outputting continuum. DOM quality along the mangrove to estuary continuum corresponded with environmental heterogeneity. Biodegradation and photo-biodegradation experiments were conducted on DOM samples over 20-days. A rapid 40–65% decrease was observed in DOC concentration in response to biodegradation. About 45% decrease of DOC concentration in photodegradation, afterward less loss in photo-biodegradation than was examined with biodegradation alone. Chromophoric dissolved organic matter (CDOM) concentrations of the continuum were in fluctuating changes during biodegradation. CDOM was preferentially removed 60–90% then increased significantly in photo-biodegradation. Photo-mediated protein-like substances were demonstrated in strong reactions during biodegradation. Compared to biodegradation alone, DOM quality can be distinctly altered during photo-biodegradation. This study demonstrates that DOM quality was gradually homogenized due to interaction with sunlight and microbes during transport from the mangrove creek to the ocean.