The present invention discloses a data transmission method, a base station, and a communication system, which are applied in the communication field. The method includes: determining to perform semi-persistent scheduling on data of a user equipment; setting a value of first information for the user equipment, so that the user equipment determines a cyclic shift value of a reference signal sequence of the user equipment according to the value of the first information; and obtaining the reference signal sequence of the user equipment, performing channel estimation according to the reference signal sequence of the user equipment, and performing demodulation on data information of the user equipment according to a channel coefficient obtained by performing the channel estimation.