In the high frequency (HF) band, a continuum bandwidth for achieving the desired range resolution is difficult to find. Besides, the power which returns from ship targets is usually lower than the levels of sea clutters at higher sea states. Therefore, it is difficult to distinguish desired targets by conventional approaches. In this paper, a multi-frequency frequency modulated continuous wave (FMCW) transceiver with optimal resource allocation based on the minimal transmit power constraint is proposed to mitigate sea clutters. Multiple-input-multiple-output (MIMO) signal processing is adopted to detect signals from different spatial directions. Simulation results show that the proposed method can provide diversity gain for discriminating targets under practical sea clutter environments.