A communication device of handling a Non Access Stratum procedure comprises instructions of accessing a first network by using the first IMSI; transmitting a first NAS request message to the first network by using the first IMSI; receiving a NAS response message comprising a timer value and a cause value from the first network; starting a timer for the first IMSI with the timer value; not transmitting a second NAS request message to the first network by using the first IMSI, if the timer is running for the first IMSI; changing from the first IMSI to the second IMSI without removing the USIM; keeping the timer running, after changing to the second IMSI; accessing a second or the first network by using the second IMSI; and transmitting a third NAS request message to the second or the first network by using the second IMSI, when the timer is running.