Based on the randomized block test with different amount of chicken manure and pig manure application (0, 15, 30, 45 and 60 t/hm²), the characteristics of accumulation and migration of Cu and Zn in soil profile, the changes in yield, quality, and the content of Cu and Zn in different organs of pepper (roots, stems, leaves, and fruits) were studied. The results showed that the content of Cu and Zn was significantly increased in the tillage layer (0-20 cm) after chicken and pig manure application. Compared to CK, the increase of Cu content reached 22.60%~66.59% and 36.13%~95.00% respectively, and the increase of Zn content reached 10.49%~39.27% and 11.18%~51.94% respectively. The increase of soil Cu and Zn content in the tillage layer (0-20 cm) after application of pig manure was greater than that of chicken manure. The content of Cu and Zn in chicken and pig manure were mainly accumulated in the soil tillage layer (0-20 cm). The highest content of Cu and Zn was 36.95 mg/kg and 137.24 mg/kg, which did not exceed the national safety level. The migration of Cu and Zn to deeper soil was significantly after 60 t/hm² chicken and pig manure application. The downward migration of Cu and Zn in chicken manure was smaller than pig manure treatment. The single fruit weight and yield of pepper significantly increased after chicken and pig manure application, and reached the highest at the 30 t/hm² application, the yield increased 24.98% and 29.04% compared to CK. The Vc content, the soluble sugar content, and the soluble protein content significantly increased, but the nitrate content significantly decreased after high amount of chicken and pig manure (60 t/hm²) application. Application of 15 t/hm² chicken manure and 60 t/hm² pig manure significantly increased Cu content in pepper fruits, but the Cu content did not exceed 20 mg/kg, which was a safe level for eating. The application of chicken and pig manure had no significant effect on the content of Zn in the fruits (from 16.35 to 20.87 mg/kg). It can be concluded that rational application of chicken and pig manure can improve soil properties, increase crop yield and quality in a short term. Although chicken and pig manure application can cause the accumulation of Cu and Zn in the tillage layer (0-20 cm), it has not caused soil pollution of Cu and Zn, and affect the safety of pepper fruits, while further monitoring is necessary if long-term application.