The invention provides a high-efficiency data center server resource autonomous control method and system, and belongs to the field of computer high-performance computing. The system comprises a resource real-time scheduling layer, wherein the resource real-time scheduling layer comprises a performance monitor, an online estimator A, a resource controller and a resource distributor, the energy consumption control layer comprises a performance monitor, an online estimator B, an energy consumption controller and a frequency regulator, and the virtual machine migration layer comprises a performance monitor, a load detector and a virtual machine migration scheduler. The method comprises three parts, namely real-time resource scheduling, energy consumption control and virtual machine migration,which are respectively and correspondingly cooperatively operated on second-level, minute-level and hour-level levels, so that the data center server achieves optimal control of performance and energy consumption. According to the method and the system, the full-cycle multi-level cloud resource scheduling management of the data center server can be realized, the energy consumption of the data center server is greatly reduced, and the cloud service quality is ensured.