Black carbon (BC) and brown carbon (BrC) have intensive impacts on atmospheric visibility and global climate change. In this study, PM2.5 samples were collected at Pudong (PD) and Qingpu (QP) of Shanghai in 2017, and characterized typical organic molecular tracers by gas chromatography-mass spectrometer. The light absorption (Abs) of carbonaceous aerosol and water-soluble organic matter was analyzed by a multi-wavelength thermal/optical carbon analyzer and a long-range ultraviolet-visible spectrophotometer. An improved two-component model integrated with both optical and chemical fingerprints of carbonaceous aerosol was applied to analyze the Abs of BC, water-soluble organic carbon (WSOC) and water-insoluble organic carbon (WISOC), with which the potential influencing factors including emission source and atmospheric aging were investigated. Results indicated that BrC contributed 19% at PD and 16% at QP of the total light absorption of the carbonaceous aerosol at 405 nm wavelength. Meanwhile, AbsWSOC(405)/AbsBrC(405) showed significant seasonal variations (27–50%) at both sites. Positive matrix factorization (PMF) analysis showed that vehicle emissions (60–61%) and biomass combustion (38–39%) were the major contributors to AbsBC(405), while biomass burning (34–40%), nitrate-relevant secondary processes (22–23%), vehicle emissions (18–19%) and biogenic SOA (13–19%) were major contributors to AbsWSOC(405). Hybrid combustion source (94–96%) had a predominant contribution to AbsWISOC(405). Statistical analysis showed that biomass burning had a great impact on the enhancement of AbsWISOC. Absorption Ångström exponent (AAE) and mass absorption efficiency (MAE) of each factor (source) using PMF analysis indicated that WSOC from combustion sources had higher AAEWSOC(350–550) values (8.11 and 8.29 for coal and biomass burning, respectively) and MAEWSOC(365) values (0.63–0.99) compared to other sources. Atmospheric aging process can lower the MAEWSOC(365) value (0.24–0.52). Overall, our study facilitates a better understanding of the relationships among source, optical properties, and atmospheric transformation processes of the carbonaceous aerosols in Shanghai.