1. Activities of wood decomposer fungi alter abiotic and biotic properties of deadwood, which are important for tree seedling regeneration on nurse logs. However, the effects were seldom evaluated experimentally. 2. In this study, we examined germination, growth, and survival of six arbuscular mycorrhizal and six ectomycorrhizal tree species on three substrates (brown rot logs, white rot logs, and soil) by seed sowing experiments in a mixed forest dominated by Pinus densiflora and Quercus serrata. We also analyzed fungal communities in these substrates by rDNA ITS1 sequencing. 3. Some significant substrate effects were found on seedling performance when comparing wood decay types, but these were not clearly consistent across mycorrhizal status of the seedlings. Nevertheless, seedlings of arbuscular mycorrhizal trees tended to show better growth on brown rot logs than on white rot logs, whereas ectomycorrhizal tree seedlings tended to survive better on white rot logs and soil compared to brown rot logs. 4. The fungal community was significantly different across three substrates. Richness of Operational Taxonomic Units (OTUs) of arbuscular mycorrhizal fungi was largest in brown rot logs, whereas OTU richness of ectomycorrhizal fungi was largest in soil. 5. Synthesis: The effects of fungal wood decay type on nurse log regeneration of tree seedlings might be partly attributable to water content and fungal communities in the logs. Particularly, rich communities of arbuscular mycorrhizal fungi in brown rot logs could assist in the growth of arbuscular mycorrhizal tree seedlings.