The pollution burdens and compositions of atmospheric brown carbon (BrC) that determine their impacts on climate-health-ecosystems have not been well studied, particularly in some mega-economic coastal areas. Herein, atmospheric BrC samples synchronously collected from urban Shanghai (SH) and Huaniao Island (HNI) in the East China Sea during winter were characterized through ultrahigh-performance liquid chromatography-diode array detector-high resolution mass spectrometry (UHPLC-DAD-HRMS). The three polarity-dependent BrC fractions exhibited significant differences in both light absorption and chromophore composition. The average light absorption coefficients of BrC subfractions at 365 nm in SH were 2.6–3.7 times higher than those in HNI. The water-insoluble BrC (WIS-BrC) and humic-likes BrC (HULIS-BrC) dominated the total BrC absorption in SH (45 ± 7 %) and HNI (43 ± 6 %), respectively. Compared with SH, the higher O/Cw, lower molecule conjugation degree, and reduced mass absorption efficiency at 365 nm (MAE365) in HNI imply a potential bleaching mechanism during the transportation oxidation process. Thousands of BrC chromophores were detected at both sites. >20 major chromophores with strong absorption were unambiguously identified in HULIS-BrC and accounted for ∼40 % of the HULIS light absorption at 365 nm at both sites. These chromophores in SH HULIS-BrC featured oxygenated aromatics and nitroaromatics, while alkyl benzenesulfonic acids with emissions from cargo ships were found in HNI HULIS-BrC. Moreover, 22 major chromophores identified in WIS-BrC included alkaloids, polyaromatic hydrocarbons (PAHs), and carbonyl oxygenated PAHs, contributing 39 % and 49 % of the WIS-BrC light absorption at 365 nm in SH and HNI, respectively. Ascertaining the molecular-specific optical properties of BrC chromophores over the mega-economic coastal area is helpful for the predictive understanding of the sources and evolution of BrC, as well as its atmospheric behavior from land to sea.