As FBMC system is considered as a possible candidate for 5G, the channel estimation of FBMC/OQAM system becomes an important research topic recently. In this paper, we study the preamble-based channel estimation and modify the estimation process on this basis. Typically, the preamble is discarded after channel estimation, but since the estimated channel response will not be exactly equal to the actual channel response, if the preamble is preserved and channel equalization is performed, the recovered signal will be different from the actual preamble. Using this difference, we construct a secondary estimation formula to improve channel estimation performance. Simulation results are provided to illustrate that the proposed method has better performance than the existing method.