Arteriovenous fistula (AVF) has the advantages of lower infection and complication rates than other access methods, and is currently the preferable vascular access method for hemodialysis patients. However, delayed maturity rate and dysfunction of AVF are frequently concerned by clinicians. Early diagnosis of dysfunctional AVF usually depends on the advanced imaging techniques, and methods in terms of effective clinical diagnosis, treatment, and prognostic evaluation are virtually rare. The mechanistic role of molecular biology in the pathogenesis of AVF dysfunction is incompletely understood. Currently, the development of genomics, transcriptomics, proteomics, and metabolomics technologies have played great roles in insight into the pathological features and clinical diagnosis of AVF dysfunction. This article summarizes and reviews the molecular biology mechanisms underlying the AVF dysfunction based on multiomics.