A ternary nanocomposite comprising phosphotungstic acid (PW12), polyethyleneimine (PEI), and graphene oxide (GO), i.e., PW12-PEI/GO, was developed as a precursor to obtain the W2C/N-rGO catalyst upon in-situ carbonization. W2C/N-rGO was applied in the deep oxidative desulfurization (ODS) of liquid fuel, and exhibited extraordinary performance due to the ultrafine W2C nanoparticles (~3–5 nm) evenly dispersed on N-rGO and the electron-donating effect of N-rGO on W2C. 4000 ppm of DBT in model oil could be completely removed within only 10 min with a remarkably high turnover frequency (168 h−1) and the lower activation energy (30.9 kJ·mol−1). Radical experiments and density functional theory calculations indicate that the ODS reaction proceeds mainly via a HO• radical mechanism. Moreover, W2C/N-rGO could be recycled for 6 successive cycles with no obvious loss of performance.