The traditional PLC system, due to the problems of its system structure and processor performance, in the process of the implementation in industrial control, often occurs the inertial downtime after a certain execution time, which influences the industrial production. The paper proposes the embedded security PLC structure model, which is based on ARM+FPGA dual processor with high performance, which can greatly reduce the probability of system failure, and improve the reliability of industrial control. This system is divided into hardware structure and software system of two parts. The hardware part adopts the double channel, which is equipped with a safety circuit, heterogeneous redundancy security architecture based on 1oo2d, and safety diagnosis circuit is designed between the two processors, determines whether a system running normally by cross detection. The software part mainly includes the build system and executive system, the build system writes PLC program into executable machine code which is called the target code, and then the execution system executes the target code.