Question How conservation and forest type affect macrofungal compositional diversity is not well understood. Even less is known about macrofungal associations with plants, soils, and geoclimatic conditions. Location Southern edge of boreal forest distribution in China, named as Huzhong Nature Reserve. Methods We surveyed a total of 72 plots for recording macrofungi, plants, and topography in 2015 and measured soil organic carbon, nitrogen, and bulk density. Effects of conservation and forest types on macrofungi and plants were compared, and their associations were decoupled by structural equation modeling (SEM) and redundancy ordination (RDA). Results Conservation and forest type largely shaped macrofungal diversity. Most of the macrofungal traits declined with the conservation intensities or peaked at the middle conservation region. Similarly, 91% of macrofungal traits declined or peaked in the middle succession stage of birch-larch forests. Forest conservation resulted in the observation of sparse, larch-dominant, larger tree forests. Moreover, the soil outside the Reserve had more water, higher fertility, and lower bulk density, showing miscellaneous wood forest preference. There is a complex association between conservation site characteristics, soils, plants, and macrofungi. Variation partitioning showed that soil N was the top-one factor explaining the macrofungal variations (10%). As shown in SEM coefficients, conservation effect to macrofungi (1.1-1.2, p < .05) was like those from soils (1.2-1.6, p < .05), but much larger than the effect from plants (0.01-0.14, p > .10). For all tested macrofungal traits, 89%-97% of their variations were from soils, and 5%-21% were from conservation measures, while plants compensated 1%-10% of these effects. Our survey found a total of 207 macrofungal species, and 65 of them are new updates in this Reserve, indicating data shortage for the macrofungi list here. Conclusion Our findings provide new data for the joint conservation of macrofungi and plant communities, highlighting the crucial importance of soil matrix for macrofungal conservation in boreal forests.