Microbial degradation of lignocellulose for resource and energy recovery has received increasing interest. Despite its obvious importance, the mechanism behind the biodegradation, especially the changes of morphological structure and surface characteristics, has not been fully understood. Here, we used three-dimensional (3D) characterization and multiscale visualization methods, in combination with chemical compositional analyses, to elucidate the degradation process of wheat straw by a white rot fungus, Phanerochaete chrysosporium. It was found that the fungal attack initiated from stomata. Lignin of the straw decayed in both size and quantity, and heterogeneity in the biodegradation was observed. After treatment with the fungus, the straw surface turned from hydrophobic to hydrophilic, and the adhesion of the straw surface increased in the fungal degradation. The morphology of the straw outer layer became heterogeneous and loose with the formation of many holes with various sizes. The wasp-tunnels-like structure of the collenchyma and parenchyma of the straw as well as the fungal hyphae interspersed inside the straw structure were clearly visualized in the 3D reconstruction structure. This work offers a new insight into the mechanism of lignocellulose biodegradation and demonstrates that multiscale visualization methods could be a useful tool to explore such complex processes.