The present invention relates to a resource allocation apparatus, resource allocation method, and non-transitory computer readable medium thereof. The resource allocation apparatus adapted for a network comprising a femto base station (BS) which communicates with the femto BS and includes a storage, a transceiver and a processor connected to the storage and the transceiver. The storage stores a random function, reuse information and fractional frequency reuse (FFR) information which records an original cell ID/frequency corresponding relation of an unoccupied partition of the network. The processor selects a time partition from the unoccupied partition according to the random function and the reuse information, changes the original cell ID/frequency corresponding relation to generate a changed cell ID/frequency corresponding relation according to the FFR information; and generates an allocation message according to the time partition and the changed cell ID/frequency corresponding relation, wherein the transceiver conveys the allocation message to the femto BS.