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Channel estimation is one of the key technologies in optical orthogonal frequency division multiplexing (OOFDM) systems. The methods based on pilot-aided for OOFDM systems are investigated in this paper. An improved channel estimation method is presented based on the least squares (LS) method. The proposed method employs the adaptive filter to improve the LS estimation by estimating and suppressing the noise in signal subspace. The channel energy is disperse in frequency domain and concentrated in time domain. Without the knowledge of statistical parameters of the channel, the new proposed method attains a significant improvement in comparison with the regular LS estimator. Simulation results show that the influence of the additive noise can be well improved by the proposed method.