The invention proposes an autonomous-management spacecraft information system and an operation method thereof. The system employs a ground and spacecraft combined working mode to execute the autonomous task management. The system comprises five hardware subsystems: a task subsystem, a propulsion control management subsystem, a looped heating management subsystem, an energy source management subsystem, and a load management subsystem. The task subsystem is used for carrying out the task analysis, task planning and task evaluation for a spacecraft, and carrying out the real-time monitoring of each subsystem. The propulsion control management subsystem, the looped heating management subsystem, the energy source management subsystem and the load management subsystem are used for task execution and the feedback of a task execution result. Therefore, the invention provides a solution for the design of a spacecraft information system which is used for the long-time and superlong-distance spacecrafts and meets the requirements of hiding performances and high real-time performances. Meanwhile, the system reduces the manual control of an astronaut, effectively reduces the task cost, and provides a technological base for the subsequent autonomous or semi-autonomous formation cooperative work among the spacecraft.