Sepsis is a systemic inflammatory response syndrome caused by infection. With complex pathogenesis and poor prognosis, it is one of the main causes of death in clinical critical patients. Phosphorylation is one of the main types of post-translational modifications. The states and changes of phosphorylation of cells or tissues can be observed through the phosphoproteomics, which can provide a new perspective for the study of the molecular mechanism of sepsis. This article mainly investigates the value of phosphoproteomics in the study of sepsis and reviews the development of phosphoproteomics and the prospect of its application in the research of sepsis. With the characteristics of phosphoproteomics, a new research approach is provided for the further study of sepsis. Its advantages are helpful to comprehensively understand the pathogenesis of sepsis.