Abstract: To know the effect of soil type on pepper growth and fruit quality formation, the pepper inbred lines ‘SJ11-3’,‘camphor tree’and‘06g19-1-1-1’were selected to study the effects of four different types of soil, moisture soil, yellow brown soil, paddy soil and pastoral soil, on the root and fruit microstructure of pepper. The study found that the pepper planted in moisture soil had the smallest proportion of xylem, and the cortical cells were the thickest. The pepper planted in pastoral soil had the most suitable proportion of xylem, and the cortical cells were the thinnest，the separation degree between the cambial cell and xylem were the lowest. The cambial cell and xylem of pepper planted in yellow brown soil separated obviously. The fruit parenchyma of pepper planted in pastoral soil increased significantly, followed by that planted in paddy soil. The fruit of pepper planted in yellow brown soil had the highest degree of fusion of the inner skin parenchyma cells. And the fruit of pepper planted in paddy soil had the most vascular bundles, followed by that planted in yellow brown soil, and that planted in moisture soil had the least. The results showed that the difference of soil type had an important effect on the microstructure of pepper roots and fruits. The pepper planted in pastoral soil had the best growth, the parenchyma parenchyma cells were thicker and the parenchyma thickening was more obvious. Therefore, the pastoral soil is more suitable for the growth of pepper and the formation of fruit taste quality.