In this paper was proposed a low complexity algorithm of the channel estimation for HF serial-tone MIMO communication channel, based on: 1) presentation of MIMO channel as a set of SIMO channels, 2) tracking of main vectors of eigenvalue decomposition (EVD) of the impulse response correlation function (IR) of a SIMO channel; 3) current MMSE estimation of IR with the approximation of the decreased rank of the correlation matrix IR This paper shows that the proposed estimation algorithm has the acceptable computational complexity and good accuracy characteristics, which were obtained by the modeling in typical conditions for the HF communication.