Traditionally considered as homogeneous innate immune cells, neutrophils are now found to exhibit phenotypic and functional heterogeneity. How to determine whether the functional changes of neutrophils are caused by activation or the result of gene reprogramming? Recent advances in multi-omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and spatial omics, have comprehensively explained the mechanism of neutrophil heterogeneity. At the same time, artificial intelligence, especially machine learning, has promoted the in-depth analysis of multi-omics. Here, we introduce the latest progress in the discovery of neutrophil subsets by omics research. We will further discuss the application of machine learning in analyzing the heterogeneity of neutrophils through omics methods. Our goal is to provide a comprehensive overview of how machine learning and multi-omics are reshaping our understanding of neutrophil biology and pathophysiology.