In order to meet the high-dependability requirement of electronic equipment for aerospace, a new method which integrating 8051 IP core and storage IP core into FPGA is proposed. After analyzing the shortcoming of traditional Triple Module Redundancy (TMR) design aiming to migrate the SEU effect on FPGA, a fault tolerance method based on TMR and readback-scrubing the configuration-data of FPGA is used. Then the reliability of this architecture is achieved in detail by Matlab tool with Markov model. Simulation results show that this FPGA architecture has higher reliability, which can meet the requirement of Aerospace electronic controller.