Tree diversity is considered a major factor promoting forest ecosystem multifunction. Although the establishment of artificial mixed afforestation patterns has been widely accepted to replace the traditional mono-plantations, knowledge about the effects of natural colonization of tree species on belowground ecosystem of coniferous plantation is lacking. In this study, we compared the Chinese fir forests which are naturally colonized with broadleaved trees (NFs) to the pure Chinese fir plantations (PFs), and examined the aboveground characteristics, and soil ecosystems including chemical property, extracellular enzyme, microbial community, and metabolomic profile. The results showed that the available nitrogen (AN), dissolved organic carbon (DOC), invertase, peroxidase and urease were increased for 14.5 %–21.5 %, 66.8 %–81.9 %, 158.0 %–331.3 %, 13.3 %–24.1 %, 21.5 %–29.9 % after the colonization of broad-leaved trees, while soil pH, cellobiohydrolase, β-cellobiosidase, and acid phosphatase, were decreased for 3.6 %–12.1 %, 12.4 %–13.6 %, 21.6 %–25.1 %, and 17.3 %–17.4 %. Compared with PFs, NFs showed higher abundance of Mortierellomycota, whereas the copies of bacteria, fungi, nifH and phoD genes, abundance of Ascomycota, and microbial network complexity in NFs were lower. After the colonization of other trees, woody plant species diversity (WSDiv) and abundance of metabolites such as oleamide, linoleamide, adrenoyl ethanolamide, and (ˆA±)-(Z)-2-(5-tetradecenyl) cyclobutanone were increased. Interestingly, most of these biotic and abiotic factors were obviously correlated with WSDiv. The PLS-PM model indicated that the increase of WSDiv responsible for the increase of AN and metabolites including oleamide, linoleamide, and adrenoyl ethanolamide, which subsequently decreased soil pH, inhibiting the growth of soil microorganisms. These suggest the potentially negative effects of NFs on soil microbiomes. By reasonably controlling woody plant species diversity, the abundance of soil microorganism in NFs could be restored. Keywords: Chinese fir; Broad-leaved trees; Soil microbiome ; Metabolites; Woody plant species diversity