Radio and clutter that cover a certain number of range-Doppler-angle cells have a major impact on the detection performance of a high-frequency surface wave radar (HFSWR) system. Especially for a small-aperture array, the angle spectrums of radio and clutter suffer from severe broadening, so the targets that are more easily submerged in the broadened radio and clutter can be hardly detected. To tackle this issue, this paper proposes an algorithm for radio decontamination and clutter suppression to enable detection of the submerged targets. First, the spatial correlation of the array is derived, and the characteristics of radio and clutter are analyzed based on angle-Doppler joint eigenvector. Then owing to the analysis, the information of radio and clutter in the main beam can be accurately estimated from that in the auxiliary beams and eliminated by subtracting it. The results of simulations and measured data indicate that the proposed method offers a significant performance improvement and has a strong robustness against the array amplitude-phase errors.