A hypervisor-based virtual machine isolation apparatus and method. The hypervisor-based virtual machine isolation method performed by the hypervisor-based virtual machine isolation apparatus includes when a hypervisor starts to run virtual machines, allocating one or more colors to each of the virtual machines, allocating a page frame corresponding to the allocated colors to the corresponding virtual machine, allocating an accessible core depending on the colors of the virtual machine, and performing isolation between virtual machines corresponding to an identical color by changing a temporal/spatial scheduling order between the virtual machines corresponding to the identical color.