High-intensity microwave (HIMW) treatment is a time-saving and environmentally friendly method widely applied in the wood processing industry. It enhances wood permeability, making it suitable for drying and impregnation modification. This study aimed to investigate the effects of HIMW on macroscopic and microscopic cracks, tracheid cell wall damage, and the chemical structure of Chinese fir [Cunninghamia lanceolata (Lamb.) Hook] wood. Through the use of a camera, optical microscope, scanning electron microscope, transmission electron microscope, Fourier-transform infrared spectroscopy, and X-ray diffraction, the morphology of cracks, cell wall damage, the chemical composition of the cell wall, and the crystalline structure of cellulose treated with HIMW were examined and analyzed. The results revealed that the initial moisture content (MC) and microwave energy density (MWED) significantly influenced the crack characteristics and cell wall structure and slightly influenced the chemical composition and crystalline structure of cellulose of the Chinese fir cell wall. HIMW treatment can produce different characteristics of wood cracks. The size and number of cracks were significantly increased with the increase in MWED, and more cracks were found in low MC. Microcracks caused by HIMW treatment tended to initiate at the ray parenchyma, resulting in the stripping of ray cells along its radial direction. Meanwhile, the cracking of adjacent cell junctions, the rupturing of the pit margo and pit torus, and cell wall parts tearing along the direction of microfibers occurred as a result of the HIMW treatment. The most severe damage to the cell walls occurred at the interface of S1/S2, S1, and ML layers, and the cell walls were torn in the S2 layer. There were no significant changes in the FTIR spectra of the HIMW treatment samples. Hemicellulose degradation occurred first, which increased with the increase in MWED. The recrystallization of cellulose and the lignin content increased because of the change in the aromatic C=O groups. As MWED increased, both the crystallinity index (CI) and cellulose crystal width (D200) of the samples that underwent HIMW treatment increased accordingly, and the number of low-MC samples was greater than that of the high-MC samples. The findings contribute to understanding the crack characteristics and damage mechanism induced by HIMW treatment on wood. This study provides valuable insights into regulating the effects of HIMW treatment and expanding its application in wood processing, such as wood drying and functionalized impregnation, according to the specific end-use requirements.