The cycling of oceanic dissolved organic carbon (DOC) is a crucial component of the global carbon cycle, yet the identification of sources and the mechanisms of its molecular transformation remain poorly understood. This study aimed to compare the isotopic and molecular composition of DOC between the oligotrophic South China Sea (SCS) and the adjacent north Pacific Ocean (NPO), tracing both its allochthonous and autochthonous sources as well as its dynamic cycling processes. DOC was collected through solid-phase extraction (SPE) from the whole water column for samples from both the SCS and NPO. Carbon content, isotopic ratios, and high-resolution Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR-MS) measurements showed that SPE-DOC contained both labile and refractory fractions. Vertical molecular composition and stable/radioactive isotope distributions from SPE-DOC jointly indicated distinct biogeochemical regimes regulating the redistributions of DOC. The production and transformation of the relatively labile DOC fractions were dominant processes in the epipelagic and mesopelagic zones (upper 1000 m). The extent of diapycnal mixing between the SCS and NPO in the bathypelagic ocean explained the different vertical distributions of refractory DOC in the studied areas. The molecular indices of polyphenol compounds, aromaticity, double bond saturation state, terrestrial mass peaks, and δ¹³C ratios of SPE-DOC indicated extra contributions from terrestrial sources, likely riverine input, in the SCS. This study sheds light on the molecular evidence of DOC sources, as well as their biotransformation and conservative mixing processes along the ocean overturning circulation.