A base station, a mobile station and a communication method thereof are provided. The base station and the mobile station are adapted for use in a wireless network. The wireless network comprises the base station and the mobile station. The mobile station connects with the base station via a physical channel. The physical channel comprises a plurality of resource units. Each resource unit comprises a sub-block. The sub-block comprises a sequence. The mobile station communicates with the base station with the sequence during the sub-block bases on a mapping relation.