A method of handling random access for a user equipment of a wireless communication system includes transmitting a plurality of repetitions of a random access preamble to a network of the wireless communication system; and monitoring a physical downlink control channel (PDCCH) in a plurality of random access response windows for receiving a random access response identified by a random access radio network temporary identifier (RA-RNTI) from the network, wherein each of the plurality of random access response windows is corresponding to one of the plurality of repetitions of the random access preamble.