Fertilization is widely acknowledged as being an essential practice to improve forest productivity in forest ecosystems. However, too little consideration has been given to the taxonomic and functional compositions of rhizosphere soil microbes and their interactions with root exudates under different fertilizer regimes in forest plantations. Here, we investigated the effects of four typical fertilizer regimes (CK, no fertilizer; CF, compound fertilizer; OF, organic fertilizer; CMF, compound microbial fertilizer) on soil microbial communities and their potential functional groups in Phoebe bournei young plantations, as well as their associations with soil physicochemical properties and root exudates. These results showed that fertilizer regimes strikingly affected the rhizosphere soil microbial community compositions and alpha diversity indices. The pathotroph was the dominant fungal guild. With the applications of three fertilizations, the relative abundances of the plant pathogen and arbuscular mycorrhiza increased. The alpha diversity of soil bacteria was highest under the OF regime, and soil fungal diversity was more powerfully affected by the amendment of CMF. Additionally, while the fungal community was simultaneously influenced by soil physiochemical factors and root exudates, the bacterial community in the rhizosphere was mostly impacted by root exudates. More importantly, the application of OF and CF induced dramatic growths of Fusarium, while CMF treatment including Bacillus suppressed the development of Fusarium via adjusting bacterial species. Overall, our findings exhibit the divergent responses of rhizosphere bacteria and fungi to fertilizer regimes in P. bournei young plantations. The application of organic fertilizer provides benefits for rhizosphere bacteria, and microbial fertilizer can help alleviate inhibition through changing pathogens.