Multi-omics technology integrates gene, protein, and metabolic information to construct comprehensive gene regulatory networks. This approach aligns with the complex nature of maize storage, characterized by its multi-component, multi-target, and multi-pathway processes. This technology offers a holistic view for exploring nutritional changes during maize storage, addressing the challenges of high costs and inefficiency in grain storage. Despite the potential of multi-omics, current research primarily focuses on the fundamental physical and chemical changes during storage, with limited application of omics technologies to understand the underlying quality change mechanisms. This paper reviews advancements in genomics, transcriptomics, proteomics, and metabolomics, and their application to maize storage. It highlights the challenges in maize storage research and underscores the potential of multi-omics to revolutionize this field. By leveraging existing research, we propose a feasible technical route for applying multi-omics to maize storage, aiming to innovate and stimulate omics research in grain storage and establish effective, green, and safe storage strategies.