Subcritical water treatment has received considerable attention due to its cost effectiveness and environmentally friendly properties. In this investigation, Chinese quince fruits were submitted to subcritical water treatment (130, 150, and 170 °C), and the influence of treatments on the structure of milled wood lignin (MWL) was evaluated. Structural properties of these lignin samples (UL, L130, L150, and L170) were investigated by high-performance anion exchange chromatography (HPAEC), FT-IR, gel permeation chromatography (GPC), TGA, pyrolysis-gas chromatography/mass spectrometry (Py-GC/MS), 2D-Heteronculear Single Quantum Coherence (HSQC) -NMR, and 31P-NMR. The carbohydrate analysis showed that xylose in the samples increased significantly with higher temperature, and according to molecular weight and thermal analysis, the MWLs of the pretreated residues have higher thermal stability with increased molecular weight. The spectra of 2D-NMR and 31P-NMR demonstrated that the chemical linkages in the MWLs were mainly β-O-4′ ether bonds, β-5′ and β-β′, and the units were principally G- S- H- type with small amounts of ferulic acids; these results are consistent with the results of Py-GC/MS analysis. It is believed that understanding the structural changes in MWL caused by subcritical water treatment will contribute to understanding the mechanism of subcritical water extraction, which in turn will provide a theoretical basis for developing the technology of subcritical water extraction.