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Paulownia fortunei, one of the world's fastest growing timber tree species, is universally applied with fertilizer as a management approach to meet the nutrient requirements for efficient cultivation. The substantial effects of fertilizer on soil microorganisms in Paulownia plantations have been empirically tested; however, the successive chronosequence of soil microbial carbon and nitrogen functional genes under different fertilizer application durations remains limited. The objective of this study was to explore the characteristics of soil microorganisms involved in carbon and nitrogen cycling and greenhouse gas (GHG) production under different fertilizer application durations. Different fertilizer treatments, i.e., the short-term group (SG) versus the long-term group (LG), and durations were applied to subtropical plantations in southern China and compared with zonal evergreen broad-leaved forests. Results showed that fertilizer treatment significantly increased the relative abundance of Acidobacteriota and the expression of nirK and nosZ. The functional groups that dominated metabolism in SG and LG treatments belonged to Actinobacteria and Acidobacteriota, respectively, suggesting that the nutrient preference of microorganisms in forest soil may change from copiotrophs to oligotrophs with increasing fertilizer application duration. Correlation network analysis showed that the communities that dominated the carbon and nitrogen cycles belonged to Actinobacteria and Acidobacteriota, respectively, and were closely related to ammonium nitrogen and available iron. Actinobacteria and Acidobacteriota were likely the major taxa that affected soil GHG production under different fertilizer application durations. We concluded that long-term fertilizer use changed the preference of microbial nutrient uptake into recalcitrant nutrients, and the sensitivity of the microbial community to nutrients gradually decreased with increasing fertilizer application time. The dominant Actinobacteria affected soil carbon and nitrogen cycles largely by stimulating denitrification to increase the release of nitrous oxide, which might lead to the loss of nitrogen components and the intensification of the GHG effect with increasing fertilizer application time. [ABSTRACT FROM AUTHOR]