Abstract: Three-dimensional fluorescence spectroscopy, combined with parallel factor (PARAFAC) analysis, canonical correspondence analysis (CCA), and structural equation model (SEM), was applied to measure the concentrations of the heavy metals and nutrients, detect the three-dimensional fluorescence spectra of dissolved organic matter (DOM), and study the response mechanism of DOM and heavy metals in urban river sediment. Surface sediment samples were collected from Huangnihe River, Xinkaihe River and Mantanghe River in Shenyang City. The average concentration of total nitrogen (TN) was ordered as Xinkaihe River>Huangnihe River>Mantanghe River, so was total phosphorus (TP). TP average concentrations were higher than 650 mg/kg in the three rivers, which attributed to heavy polluted status. According to the correlation analysis, Cu, Ni and Cr were homologous in Huangnihe River, As, Cd and Hg were homologous in Xinkaihe River, and As and Zn were homologous in Mantanghe River. Based on PARAFAC analysis, five fluorescent components were extracted from DOM in the three rivers, namely, terrestrial humus (C1), fulvic-like (C2 and C3), humic-like (C4), tryptophan-like (C5), among which the abundance of C1 accounted for 30.31% of the total abundance, and C2 and C3 accounted for 37.76%. Obviously, terrestrial humus and fulvic-like were the main components of DOM. DOM in Huangnihe River and Xinkaihe River were deeply affected by the allochthonous, while DOM in Mantanghe River by the autochthonous. Based on CCA, C3, C5, Cr and Pb were the characteristic factors affecting Huangnihe River sediment, Hg was the important factor affecting Xinkaihe River sediment, and TP, As and Zn were the characteristic factors affecting Mantanghe River sediment. Based on SEM analysis, the weights of TN, TP, C1, C2, C3 and C5 to heavy metals was 25.46%, 22.16%, 17.52%, 15.42%, 9.11% and 10.33%, respectively, indicating that TN and TP were the main influencing factors of the heavy metals. The path coefficient of the nutrients was -0.18 for the heavy metals, whose path coefficients for Hg, As, Zn and Cd were -2.83, -1.69, -1.91 and -3.24 respectively, which indicated that the nutrients had homology with Hg, As, Zn and Cd. Furthermore, the path coefficient of DOM was 0.11 for the heavy metals, whose path coefficients for Pb and Cr were 1.58 and 1.00, which suggested that DOM had homology with Pb and Cr.