Abstract: We investigated the responses and underlying mechanisms of community composition, and function group of fungi in yellow clayey paddy soil to different long-term fertilization, which may provide scientific basis for rational fertilization and sustainable development in agriculture ecosystems. There were four treatments, including control (CK), inorganic fertilizer (NPK), inorganic fertilizer combined with manure (NPKM), and inorganic fertilizer combined with straw (NPKS). Illumina high-throughput sequencing and FUNGuild were performed to investigate the fungal community structure and functional group, respectively. Ascomycota, Basidiomycota, and Zygomycota were identified as the three dominant ones. The proportion of Ascomycota in NPKM and NPKS were significantly lower (49% and 47%, respectively) compared with CK (71%) and NPK (74%) treatments, with the main reduced orders of Hypocreales, Pleosporales and Eurotiales. While there was higher relative abundance of Basidiomycota in NPKM and NPKS (18% and 28%) compared to CK (14%) and NPK (10%), the orders with enhancement were Tremellales, Trechisporales, and Agaricales. The ratio of Basidiomycota was decreased with sole inorganic fertilizer. Moreover, the relative abundance of Zygomycota was increased after 33 years of fertilization, which was dominated by Mortierellales and Basidiobolales at order level. Diversity indices including Shannon, Simpson, Chao1 and ACE were all significantly declined in NPK compared with CK, NPKM and NPKS treatments, whereas Chao1 index and ACE index in NPKM and NPKS were higher than that in CK and NPK. Saprotroph was the main fungal functional group across all the four treatments (48%-57%). Higher proportion of symbiotroph fungi was identified in soils with NPKS and NPKM (17%) in comparison to CK and NPK. The main guilds with the increasing proportion were arbuscular mycorrhizal fungi and ectomycorrhizal fungi. However, significantly higher proportion of animal pathogen fungi were detected in NPK (10%) than other treatments. Redundancy analysis (RDA) showed that moisture, salinity and porosity in soil were more strongly related with fungal community composition and fungal functional composition than soil organic matter and total nitrogen. Our results suggest that sole application of inorganic fertilizer results in great changes in fungal community compositions and the hazard of over production of pathogen fungi, whereas combined organic-inorganic fertilization would be beneficial to maintain the healthy environment through increasing fungal diversity and the ratio of symbiotrophic fungi in yellow clayey paddy soil.