1. A method for analyzing root causes of relating performance issues among virtual machines (VMs) to physical machines (PMs), adapted to a physical data center comprising: applying an application-level dependency discovery and anomaly detection to find an application-level dependency in one or more VMs running on a plurality of PMs in the physical data center, and generate an application-level topology with anomaly; transferring the application-level topology with anomaly to a VM-level dependency; transferring the VM-level dependency to a PM-level dependency via a physical and virtual resource mapping, and generating a group of event sets; and generating a prioritized event list by prioritizing the group of event sets.