Due to the fluctuation of the signal-to-noise ratio (SNR) and the single snapshot case in the MIMO HF sky-wave radar system, the accuracy of the online estimation of the mutual coupling coefficients matrix of the uniform rectangle array (URA) might be degraded by the classical approach, especially in the case of low SNR. In this paper, an Online Particle Mean-Shift Approach (OPMA) is proposed, which is to get a relatively more effective estimation of the mutual coupling coefficients matrix with the low SNR. Firstly, the spatial smoothing technique combined with the MUSIC algorithm of URA is introduced for the DOA estimation of the multiple targets in the case of single snapshot which are taken as coherent sources. Then, based on the idea of the particle filter, the online particles with a moderate computational complexity are used to generate some different estimation results. Finally, the mean-shift algorithm is applied to get a more robust estimate of the equivalent mutual coupling coefficients matrix. The simulation results demonstrate the validity of the proposed approach in terms of the success probability, the statistics of bias, and the variance. The proposed approach is more robust and more accurate than the other two approaches.