Angle estimation for low-altitude targets above the sea surface is a challenging problem due to multipath interference from surface reflection signals, and various approaches have been proposed. This paper proposes a matrix pencil method with multiple apertures. The matrix pencil method effectively responds to dynamic scenarios because it performs better when using a single snapshot than other methods. Also, employing multiple apertures is more economical than using one large aperture. Therefore, we propose a computationally efficient approach using this method and structures. The proposed two-stage MP method incrementally improves the resolution in two stages: in stage 1, we extract the denoised signals at each aperture level, and in stage 2, we further improve the resolution with those signals. In comparison with the angular resolution defined by the half-power beamwidth (HPBW) of a uniform linear array (ULA) antenna with an equivalent number of arrays, the proposed method demonstrated a superior resolution of less than 0.087 of the HPBW at a high signal-to-noise ratio (SNR) of 40 dB, and less than 0.31 of it even at a relatively low SNR of 15 dB, based on 90% of the resolving probability. For the multipath problem, the proposed scheme has the advantage of not requiring prior geometric information, and its performance is demonstrated through simulations to be better than the adaptive beamforming method and the composite monopulse method.