In this paper, the channel estimation and signal-to-noise ratio (SNR) estimation technique of single-carrier frequency domain equalization (SC-FDE) system under low SNR in aeronautical multipath channel are studied, a SNR estimation algorithm which is easy to implement in engineering and an improved LS channel estimation algorithm based on Kalman filter using minimum error entropy (MEE-KF) are proposed. This paper first introduces the SC-FDE system and introduces the principle of MEE-KF, and then, the channel estimation flow based on MEE-KF is obtained by combining it with the traditional LS channel estimation algorithm, which makes the estimation results perform better. Simulation results show that after getting more accurate noise variance, the channel estimation results can better follow the changes of the channel after MEE-KF processing, so as to resist the doppler frequency offset effect and make the channel estimation results more accurate, that is the channel response results of the data part can be closer to the real situation, so that the communication performance of SC-FDE system has also been greatly improved.