In this paper, we consider the problem of preamble design in multiple-input multiple-output (MIMO) systems employing offset quadrature amplitude modulation based filter bank multicarrier (OQAM/FBMC) and propose a preamble optimization method for the frequency division multiplexing (FDM)-structured preamble. Specifically, we formulate an optimization problem to determine the frequency division multiplexed preambles, where the objective is to minimize the mean square error (MSE) of the channel estimation, subject to the constraint on the transmit energy. For two transmit antennas, we find the relationship between preambles and the intrinsic interference from neighboring symbols to achieve the minimum channel estimation MSE, and derive the optimal closed-form solution. For more than two transmit antennas, the constrained preamble optimization problem is nonconvex quadratic. Therefore, we convert the original optimization problem into a quadratically constrained quadratic program (QCQP) and obtain the suboptimal solution by relaxing the nonconvex constraint. Simulation results demonstrate that, in terms of MSE and bit error rate (BER) performances, the proposed method outperforms the conventional FDM preamble design method at all signal-to-noise ratio (SNR) regimes and outperforms the interference approximation method-complex (IAM-C) preamble design method at low to medium SNR regimes with lower preamble overhead.