Intrinsic imaginary interference (IMI) induced by chromatic dispersion (CD) and polarization mode dispersion (PMD) seriously degrades the performance of optical orthogonal frequency division multiplexing offset-quadrature amplitude modulation (O-OFDM/OQAM) systems. Therefore, effective channel estimations are required for such systems to maintain good transmission performance. In the previous publications, both the full loaded (FL) and the half loaded (HL) frequency-domain channel estimation methods for polarization-division-multiplexed (PDM) coherent optical OFDM/OQAM (CO-OFDM/OQAM) systems have been proposed. However, for these frequency-domain methods, the channel frequency-domain responses caused by the correlation of the amplified spontaneous emission (ASE) noise are not considered. In this paper, we systematically discuss the frequency-domain channel transmission model for PDM CO-OFDM/OQAM systems. With the analysis of the correlation of the ASE noise, we propose a combined intra symbol frequency-domain averaging (CISFDA) channel estimation method for PDM OFDM/OQAM systems. Compared with the full-loaded frequency-domain channel estimation (FL-FD) method, the CISFDA method promotes the system robustness against the ASE noise and fiber nonlinear effect significantly. The proposed method is validated by numerical Monte Carlo simulations of the PDM CO-OFDM/OQAM system. Our new algorithm outperforms the FL-FD method in the 36 Gb/s PDM OFDM CO-OFDM/OQAM system, and the transmission distance is improved by 500 km with the bit-error-rate (BER) target at 3.8×10-3.