The multiplicity-edited heteronuclear single quantum correlation (ME-HSQC) NMR method is widely used for the structural characterization of marine dissolved organic matter (DOM), which is a complex molecular mixture comprising millions of individual compounds. However, the standard ME-HSQC suffers from significant signal cancellation and subsequent loss of crucial structural information due to the overlap between CH3/CH (positive) and CH2 (negative) cross-peaks in overcrowded regions. This study introduces nonuniform sampling in frequency-reversed ME-HSQC (NUS FR-ME-HSQC), highlighting its remarkable potential for the comprehensive structural characterization of marine DOM. By reversing the frequency of CH2 cross-peaks into an empty region, the FR-ME-HSQC method effectively simplifies the spectra and eliminates signal cancellation. We demonstrate that nonuniform sampling enables the acquisition of comparable spectra in half the time or significantly enhances the sensitivity in time-equivalent spectra. Comparative analysis also identifies vulnerable CH2 cross-peaks in the standard ME-HSQC that coincide with CH3 and CH cross-peaks, resulting in the loss of critical structural details. In contrast, the NUS FR-ME-HSQC retains these missing correlations, enabling in-depth characterization of marine DOM. These findings highlight the potential of NUS FR-ME-HSQC as an advanced NMR technique that effectively addresses challenges such as signal overcrowding and prolonged experimental times, enabling the thorough investigation of complex mixtures with implications in several fields, including chemistry, metabolomics, and environmental sciences. The advantages of NUS FR-ME-HSQC are experimentally demonstrated on two solid-phase-extracted DOM (SPE-DOM) samples from the surface and deep ocean. With this new technology, differences in the composition of DOM from various aquatic environments can be assigned to individual molecules.