The work aims to guarantee the integrity of pecan kernel and reduce the damage rate by changing the processing procedure of pecan and optimizing the system structure and control. With PLC as the control core component and based on the intelligent control system software design, the system realized the automatic control of the whole process of primary pecan shell cracking, screening, winnowing, secondary high-speed impact shell cracking, re-screening, winnowing, color selection and packaging. Through the variable-speed feeding and the appropriate algorithm, the packaging accuracy was improved. The damage rate test indicated that, in the perfect pecan kernels, the kernel surface was bright and free from obvious scars, and most of them were round. The average damage rate of the kernel was 6.25%. The kernel damage rate was low. The shell cracking quality of the system was verified. The damage rate test and packaging accuracy experiment results show that, the system meets the design requirements. At present, the system has been widely applied in production.