Assessing the degradation degree of waterlogged wooden cultural relics often presents challenges such as severe sampling damage and lengthy testing processes. To address these problems, this study proposes a comprehensive quasi-nondestructive evaluation method for assessing the degradation degree of waterlogged wooden shipwrecks. Four representative Chinese shipwrecks—Cixi from the Yuan Dynasty, and Wanjiao No.1, Xiaobaijiao No.1, and Changjiangkou No.2 from the Qing Dynasty—were selected as research objects. On-site sampling was conducted using hand-sliced sections and growth cone to collect specimens from the surface and different depths of ship components. The wood anatomical structures of the hand-sliced sections were analyzed to identify tree species and determine their degradation grade. Additionally, Fourier transform infrared (FTIR) spectroscopy was applied to the growth cone samples. The lignin-to-carbohydrate (L/C) ratio, derived from the characteristic peak intensities of lignin and polysaccharides, was calculated to compare the polysaccharide composition at different depths within the same sample. The results indicate that the surface degradation of ship components from Cixi, Xiaobaijiao No.1, and Changjiangkou No.2 is mainly moderate, while Wanjiao No.1 exhibits slight to moderate degradation. The anatomical structures of growth cone samples from Cixi and Changjiangkou No.2 at different depths show relatively uniform and slight degradation. There is no significant difference in L/C values among different depths. These findings demonstrate that the proposed quasi-nondestructive approach provides reliable technical support for accurately assessing the degradation degree of waterlogged wooden cultural relics.