SRAM(static random access memory)-based FPGA(field programmable gate array), owing to its large capacity, high performance, and dynamical reconfiguration, has become an attractive platform for So PC(system on programmable chip) development. However, as the configuration memory and logic memory of the SRAM-based FPGA are highly susceptible to SEUs(single-event upsets) in deep space, it is a challenge to design and implement a highly reliable FPGA-based system for spacecraft, and no practical architecture has been proposed. In this paper, a new architecture for a reliable and reconfigurable FPGAbased computer in a highly critical GNC(guidance navigation and control) system is proposed. To mitigate the effect of an SEU on the system, multi-layer reconfiguration and multi-layer TMR(triple module redundancy) techniques are proposed, with a reliable reconfigurable real-time operating system(Space OS) managing the system level fault tolerance of the computer in the architecture. The proposed architecture for the reconfigurable FPGA-based computer has been implemented with COTS(commercial off the shelf) FPGA and has firstly been applied to the GNC system of a circumlunar return and reentry flight vehicle. The in-orbit results show that the proposed architecture is capable of meeting the requirements of high reliability and high availability, and can provide the expressive varying functionality and runtime flexibility for an FPGA-based GNC computer in deep space. Due to its large capacity, high performance, and dynamical reconfiguration, has become an attractive platform for SoC (system on programmable chip) development. However, as the configuration memory and logic memory of the SRAM-based FPGA are highly susceptible to SEUs (single-event upsets) in deep space, it is a challenge to design and implement a highly reliable FPGA-based system for spacecraft, and no practical architecture has been proposed. In this paper, a new architecture for a reliable and reconfigurable FPGA based on a critical critical GNC (guidance navigation and control) system is proposed. To mitigate the effect of an SEU on the system, multi-layer reconfiguration and multi-layer TMR (triple module redundancy) techniques are proposed, with a reliable reconfigurable real-time operating system (Space OS) managing the system level fault tolerance of the computer in the architecture. The proposed architecture for the reconfigurable FPGA-based computer has been implemented with COTS (commercial off the shelf) FPGA and has been applied to the GNC system of a circumlunar return and reentry flight vehicle. The in-orbit results show that the proposed architecture is capable of meeting the requirements of high reliability and high availability, and can provide the expressive varying functionality and runtime flexibility for an FPGA-based GNC computer in deep space.