AbstractDuring probe‐to‐Earth superior conjunction, deep space communication channels will suffer from solar scintillation, leading to amplitude attenuation of received signals. This study aims to obtain the channel state information (CSI) on deep space channels affected by solar scintillation. Classical least squares (LS) and minimum mean squared error (MMSE) methods are adopted to perform channel estimation and compensate for the channel fading. Simulation results indicate that under the effect of solar scintillation, performing channel estimation technology can significantly improve bit error rate (BER) performance compared to systems without CSI, and the MMSE algorithm outperforms the LS for both BER and normalized mean squared error (NMSE). In addition, we also find that pilot density, geometric parameters, and the outer scale of solar wind turbulence has great influence on the estimation performance.