The mission payload for navigation in unmanned system serve as the linchpin for achieving autonomous operation, precision mission execution, and adaptability across diverse application scenarios. The satellite navigation payloads are characterized as intensiveness of technology, diversification of types and complication of functions in the current landscape. The satellite navigation equipment is custom-designed in specific mission requirements. However, the development of terminal-based equipment suffers from high costs, low technology reuse rates, tightly coupled structures, and complex system interconnections. The mission capabilities are difficult to reconfigure and redefine effectively. We propose a novel navigation payload scheme based on software and hardware decoupling in this paper, which is designed by using cloud-edge-based architecture. By comparing with traditional architectures, the proposed architecture can achieve dynamic matching between algorithms and mission requirements by fully exploiting software efficiency while leveraging constrained hardware resources.