Regarding new requirements of a missile borne computer in high-performance and low-cost requirements. a missile borne flight control computer with ZYNQ-7000 as the core processor is designed,which greatly improves the product's computing performance, power consumption and cost. A software-hardware co-design method is proposed to realize flexible customization of the common peripheral resources. This article introduces the hardware and software design scheme of the missile borne computer in detail, and introduces the design ideas of each circuit module, software design ideas and system workflow. After the hardware-in-loop simulation, it is verified that the missile-borne computer functions normally, the timing design is correct, and the control model solving meets the requirements of the control system.