Myelodysplastic syndrome (MDS) is a heterogeneous clonal myeloid malignancy with a variable prognosis. Some myeloid-related gene alterations have been found to be associated with the diagnosis and prognosis of MDS. As a result, multiple myeloid-related gene mutations have been added to International Working Group for Prognosis in MDS (IWG-PM) and other MDS prognosis evaluation systems as diagnostic and prognostic indications. Further research using the variable allele frequency (VAF) detection technique demonstrated that myeloid-related genes evolve dynamically during the course of MDS with some regularity. Furthermore, significant relevance have been found between the VAF evolution of particular myeloid-related genes and MDS subtypes, risk classification, and prognosis. This article provides an overview of the application of VAF of myeloid-related gene mutations in MDS research, highlighting the critical role of gene mutation VAF in MDS subtype categorization, risk stratification, and therapy response assessment.