In order to investigate the composition and transformation of clay minerals in soil nanoparticles under the combination of Chinese milk vetch and different proportions of reduced chemical fertilizer, the long-term experiment was conducted in Nanxian County, Hunan Province, where Chinese milk vetch returning (MV) was combined application with 100%, 80%, 60% and 40% (F100, F80, F60 and F40) ratio fertilizer, and then the soil was divided into four particle grades (> 2000 nm, 2000-450 nm, 450-100 nm and 100-25 nm), to investigate the distribution characteristics and transformation rules of clay minerals in different particle grades. Result showed that (1) Soil particles decreased from > 2000 nm to 100-25 nm, the relative content of illite in 2000-450 and 450-100 nm particles was reduced by 8%-11%, the 1.4nm minerals and vermiculite in 100-25 nm particles were rarely or even disappeared, the content of free iron and amorphous iron increased, and was highest in 100-25 nm particles. (2) Under the combined application of Chinese milk vetch and chemical fertilizer, the transformation rules of minerals showed obvious difference before and after the chemical fertilizer application rate of 80%. Fertilizer was reduced from 100% to 80%, the relative content of kaolinite increased by 14.1%-51.2%, while the relative content of illite decreased by 3.6%-11.7%. and then continued to reduce the fertilizer dosage, the relative content of kaolinite decreased by 13.7%-28.8%, and the relative content of illite increased by2.6%-18.5%. (3) With the decrease of chemical fertilizer dosage, the content of free iron had no consistent change pattern, but the content of amorphous iron increased significantly at first and then decrease, and reached a maximum of 145.31g/kg at MV+F80 in 100-25 nm nanoparticles. So the conversion of kaolinite, illite and amorphous iron in the soil particles was significantly correlated with the reduction of fertilizer application, and the effect was most significant at the 20% reduction of fertilizer application.