The molecular transformation and recalcitrance of dissolved organic nitrogen (DON) are critical for understanding the DON distribution, reactivity continuum and N cycling from coastal to pelagic ocean, but remain poorly understood. To answer these unknowns, we conducted a 548-day incubation experiment using photo-irradiated DON and none photo-irradiated DON enriched from coastal waters. We integrated fluorescence spectroscopy, stable isotopes, and FT-ICR-MS to examine the transformation of DON molecules. Results showed that photo irradiation treatment did not produce refractory DON (RDON) molecules but significantly enhanced bioactivity by reducing DON aromaticity and elevating H/C ratios. The molecular transformation of the none photo-irradiated DON followed a pathway from CHON2/CHON3→CHON1, whereas the photo-irradiation changed the transformation pathway to CHON1/CHON3 → CHON2, and notably accelerated the accumulation of RDON molecules. Despite distinct differences in initial molecular and isotope compositions, long-term microbial processing ultimately drove the convergence in molecular and isotopic compositions between the two incubations, both accompanied with increasing RDON proportions. With these evidences put together, we proposed that photo-irradiation behaves as a "latch" regulating DON bioactivity and transformation pathways, while microbial processes determine the ultimate molecular and isotopic compositions, reactivity, and RDON production, revealing key mechanisms in photo-microbial synergy within coastal DON cycling.