In the past, several frequency-domain channel-estimation methods were proposed for coherent optical orthogonal frequency division multiplexing systems, which use offset-quadrature-amplitude modulation (CO-OFDM-OQAM). A common challenge for these methods is that the training sequences they use, even though they increase the magnitude of the pseudo-pilots, can make the peak-to-average power ratio (PAPR) of the signal worse. To address this problem, an innovative modified frequency-domain channel estimation method is designed and investigated for a polarization-division-multiplexed CO-OFDM-OQAM system that uses dual-dependent pilots. The operating principle of this new method is described in detail. Then, its PAPR performance and channel-estimation capability are examined using numerical simulations. The proposed method not only ensures a sufficiently large magnitude of the pseudo-pilot but also does not seriously degrade the PAPR of the signal. It is also found that the magnitude of its pseudo-pilot (2.3136) exceeds that of the interference approximation method with real pilots (1.1086), and it is only slightly worse than that of the enhanced IAM with complex pilots (2.6074). The PAPR of the new method (max 11.4 dB) is much lower than that of other frequently used methods. Finally, the channel-estimation capability of the proposed method is validated for both back-to-back and long-distance transmission scenarios. Furthermore, the BER performance of several different channel-estimation methods is also compared. The obtained results confirm the above observations.