The biodegradation path and mechanism of wood varies depending on diverse fungi and tree species, as fungi possess selectivity in degradation of versatile wood components. This paper aims to clarify the actual and precise selectivity of white and brown rot fungi and the biodegradation effects on different tree species. Softwood (Pinus yunnanensis and Cunninghamia lanceolata) and hardwood (Populus yunnanensis and Hevea brasiliensis) were subjected to a biopretreating process by white rot fungus Trametes versicolor, and brown rot fungi Gloeophyllum trabeum and Rhodonia placenta with various conversion periods. The results showed that the white rot fungus Trametes versicolor had a selective biodegradation in softwood, which preferentially convert wood hemicellulose and lignin, but cellulose was retained selectively. Conversely, Trametes versicolor achieved simultaneous conversion of cellulose, hemicellulose and lignin in hardwood. Both brown rot fungi species preferentially converted carbohydrates, but R. placenta had a selectivity for the conversion of cellulose. In addition, morphological observation showed that the microstructures within wood changed significantly, and the enlarged pores and the improved accessibility could be beneficial for the penetration and accessibility of treating substrates. The research outcomes could serve as fundamental knowhows and offer potentials for effective bioenergy production and bioengineering of bioresources, and provide a reference for further application of fungal biotechnology.