The invention discloses a pilot sequence structure in an MIMO-OFDM / OQAM (Multi-input Multi-output-Orthogonal Frequency Division Multiplexing / Offset Quadrature Amplitude Modulation) system and a channel estimation method. Different pilot sequences are adopted by different antennae, the pilot sequence of each antenna is composed of three segments of symbol sequences, the length of each symbol sequence accords with the number of subcarriers, wherein the first segment of symbol sequence and the third segment of symbol sequence are all-zero symbol sequences, pilot signals are arranged at equal intervals in the second segment of symbol sequence, the pilot signal positions of all the antennas are different, the symbols of the pilot signals are randomly chosen from a candidate symbol set, and the interval between the pilot signals is two times the number of the antennas. The channel estimation method put forward by the invention can be utilized to eliminate inter-symbol interference and inter-subcarrier interference caused by multipath interference, so that the accuracy of the channel estimation of the MIMO-OFDM / OQAM system can be increased. Meanwhile, the pilot sequence structure decreases the peak-to-average power ratio of transmitted signals, and can meet the linear dynamic range of a radio frequency front-end high power amplifier and decrease the linearity requirement of the MIMO-OFDM / OQAM system on the high power amplifier.