To elucidate the effect of climate warming on the soil heterotrophic microbial community in warm-temperate, evergreen broad-leaved forests, we conducted a soil-warming experiment in a secondary forest located in the city of Higashi-Hiroshima in western Japan. We established ten trench plots (1 m × 1 m) with root barriers to prevent root regrowth in the forest. The plots were divided into warming and control treatments. Infrared heaters were used to increase the soil temperature of the warming plots by about 2.5°C for three years. We used phospholipid fatty acid (PLFA) analysis to examine the composition of the soil heterotrophic microbial community. There were no significant differences in the total content of PLFAs (TotPLFAs) and fungal PLFAs (FungPLFAs) between the warming and control plots. However, warming caused an increase in the amount of bacterial PLFAs (BactPLFAs), the result being a lower ratio of FungPLFAs to BactPLFAs (F/B ratio) in the warming plots. The results indicated that the soil heterotrophic microbial community in this warm-temperate, evergreen broad-leaved forest was sensitive to climate warming.