A communication system, user device thereof, and a synchronization method thereof are provided. The communication system includes a user device and a wireless network. A ciphering configuration information is transmitted to a user device. The user device and wireless network re-establishing the radio link control (RLC) entity of logical link. The user device changes to the new ciphering configuration immediately following the re-establishment of RLC entity according to the received ciphering configuration information and the wireless network changes to the new ciphering configuration.