The emergence of ultra-wideband (UWB) and high-throughput signals has necessitated advancements in data sampling technologies1. Sub-Nyquist sampling methods, such as the modulated wideband converter (MWC) and compressed auto-correlation spectrum sensing (CCS), address the limitations of traditional analog-to-digital converters (ADCs) by capturing signals below the Nyquist rate. However, these methods face challenges like spectral leakage and complex hardware requirements. This paper proposes a novel super-resolution generalized eigenvalue method that integrates the matrix pencil method with the Chinese Remainder Theorem (CRT) to enhance signal processing capabilities within a true sub-Nyquist framework3. This approach aims to improve frequency resolution and accuracy in high-frequency signal extraction, with potential applications in telecommunications, radar, and medical imaging.