Microplastics (MPs) are characterized by small particle sizes (<5 mm) and are widely distributed in the soil environment. To date, little research has been conducted on investigating the effects of MPs on the soil microbial community, which plays a vital role in biogeochemical cycling. In the present study, we investigate the influence of two particle sizes of MPs on dissolved organic carbon (DOC) and its relative functional groups, fluxes of greenhouse gases (GHGs), and the bacterial and fungal communities in fertilized soil. The results showed that a 5% concentration of MPs had no significant effect on soil DOC, whereas the formation of aromatic functional groups was accelerated. In fertilized soil, the existence of MPs decreased the global warming potential (GWP) as a result of a reduction in NO emissions during the first three days. A potential mechanism for this reduction in NO emissions might be that MPs inhibited the phylum Chloroflexi, Rhodoplanes genera, and increased the abundance of Thermoleophilia on day 3. An increase in NO emissions was observed on day 30, mainly due to the acceleration of the NO reduction and a decrease in the abundance of Gemmatimonadacea. The CH uptake was significantly correlated with Hyphomicrobiaceae on day 3 and Rhodomicrobium on day 30. In soil with MPs, Actinobacteria replaced Proteobacteria as the dominant phylum. Larger MPs increased the richness (Chao1) and abundance-based coverage estimators (ACE) and diversity (Shannon) of the bacterial community on day 3, whereas these decreased on day 30. The richness and diversity of the fungal community were also reduced on days 3 and 30. Smaller MPs increased the community richness and diversity of both bacterial and fungal communities in fertilized soil. Our findings suggest that MPs have selective effects on microbes and can potentially have a serious impact on terrestrial biogeochemical cycles.