Abstract: To address the issues of complex scientific payload operation modes, high individual requirements, and difficulties in lightweight design for Queqiao-2 relay satellite, a design method based on subsystem integration optimization was adopted. A scientific payload manager was configured to achieve tightly coupled integration, unified power supply and distribution, data processing, and interface management. Meanwhile, digital simulation verification and on-orbit calibration planning were carried out in parallel. Through simulations and ground verification tests, it has been demonstrated that this method effectively enhances system integration, reliability, and fault handling capabilities, meeting the mission requirements of up to eight years in orbit. The results show that the developed payload system solution, characterized by high integration, high reliability, and long-term operability, can provide an important reference for the design of payload systems for future Chinese lunar and deep space exploration missions.