Wood is easily affected by decay fungi, mildew fungi, insects, water, UV, and other factors when used outdoors. In particular, mildew on the surface of wood negatively affects the appearance and practical use of wood or wood-based engineered products. In recent years, as a class of popular crystalline materials, metal–organic frameworks (MOFs) have been widely applied in electrochemistry, adsorption, anti-mildew efforts, and other areas. In this study, we first grew a Co-based metal–organic framework (Co-MOF) in situ on a wood surface and subsequently converted the Co-MOF in situ into a cobalt–nickel double hydroxide layer, which formed micro- and nanohierarchical composite structures on the wood surface. The low surface energy of the CoNi-DH@wood was further modified via impregnation with sodium laurate to obtain the superhydrophobic wood (CoNi-DH-La@wood). We characterized the microstructure, chemical composition, water contact angle, and anti-mold properties of the CoNi-DH-La@wood using SEM, XRD, XPS, water contact angle tests, and anti-fungal tests. The SEM, XRD, and XPS results confirmed that the metal–organic framework was coated on the wood surface, with the long-chain sodium laurate grafted onto it. The CoNi-DH-La@wood had a water contact angle of 151°, demonstrating excellent self-cleaning ability. In addition, the fabricated superhydrophobic balsa wood exhibited excellent chemical and environment stability. Lastly, the CoNi-DH-La@wood exhibited excellent anti-mildew properties in a 30-day anti-mildew test because the superhydrophobic coating was successfully coated on the wood surface. In summary, this work presents an attractive strategy for obtaining wood with superhydrophobic properties at room temperature, thereby endowing the wood or wood-based engineered products with excellent anti-mildew properties.