Changes of the above-ground vegetation by logging in tropical rain forests may influence soil microbial communities, which are important in mediating soil organic matter decomposition and nutrient cycling. We studied how soil microbial communities changed with increasing magnitude of forest degradation in logged-over Bornean rain forests. The 16S and ITS amplicon sequencing was applied to bacterial and fungal DNA in topsoils (10 cm depth) from a total of 35 forests which differed in the magnitude of forest degradation. PCoA analysis was applied to bacterial and fungal community data at a phylum-level resolution. PCoA axis-1 values significantly correlated with vegetation intactness (community compositional similarly of a given plot with a pristine forest) for both bacteria and fungi, suggesting that bacterial and fungal communities changed concomitantly with the vegetation change. Acidobacteria and Proteobacteria well contributed to bacterial PCoA ordination, while Ascomycota, Basidiomycota, and Mucoromycota contributed to fungal PCoA ordination. The relationship between soil environmental factors and soil microbial communities was also found. These results suggested that changes of aboveground vegetation would directly affect the substrate of microbial decomposition, and indirectly affect microbial communities through the changes of soil environmental factors.