A method of handling at least one secondary cell of a mobile device in a wireless communication system is disclosed. The mobile device is managed by a first network of the wireless communication system. The method comprises releasing the at least one secondary cell, after receiving a handover command from the first network, wherein the handover command indicates the mobile device to hand over from the first network to a second network of the wireless communication system; wherein the second network conforms to a 3GPP standard with a version equal to or earlier than the 3GPP Rel-9, and the first network conforms to the 3GPP standard with a version equal to or later than the 3GPP Rel-10.