The copper complexing of dissolved organic matter released from hydrochar (HDOM) affects the former's environmental behavior. In this study, how hydrothermal temperatures (180, 220 and 260 °C) influence the molecular-level constitutions and Cu(II) binding features of HDOM were elucidated via fourier transform ion cyclotron resonance mass spectrometry and multi-spectroscopic analysis. The findings demonstrated that the almost HDOM molecules had the traits of lower polarity and higher hydrophobicity. As the hydrothermal temperature increased, the molecules with particularly high relative strength gradually disappeared, average molecular weight, percentages of CHON and aliphatic compounds of HDOM reduced while the percentages of CHO and aromatic compounds increased. In general, the fluorescence quenching of Cu(II) weakened as hydrothermal temperature rose and the Cu(II) binding stability constants of fluorophores in HDOM were 4.50–5.31. In addition, the Cu(II) binding order of fluorophores in HDOM showed temperature heterogeneities, and polysaccharides or aromatic rings of non-fluorescent substances had the fastest responses to Cu(II) binding. Generally, fluorescent components tend to bind Cu(II) at relatively trace concentrations (0–40 µmol/L), whereas non-fluorescent substances tend to the bind Cu(II) at relatively higher concentrations (50–100 µmol/L). This study contributed to the prediction of the potential environmental behaviors and risks of Cu(II) at the molecular level after hydrochar application.