Embodiments of the present application provide a method for transmitting control information, a user equipment and a base station. The method includes: acquiring a resource index of a physical uplink control channel PUCCH; acquiring a sequence index of an orthogonal sequence of the PUCCH according to the resource index, and acquiring the orthogonal sequence according to the sequence index; acquiring a cyclic shift of a reference signal of the PUCCH according to the sequence index; and transmitting the UCI to the base station on the PUCCH according to the orthogonal sequence and the cyclic shift. In the embodiments of the present application, a cyclic shift of a reference signal of a PUCCH channel for transmitting UCI is acquired according to a sequence index, and the UCI is transmitted on the PUCCH according to the cyclic shift and a corresponding orthogonal sequence, which can enhance transmission performance of the UCI.