Background Epigenetics plays a significant role in the pathogenesis of autoimmune diseases (ADs) and has garnered considerable attention in related research fields. Recent studies have shown substantial progress in understanding the association between epigenetics and autoimmune diseases. However, there is a lack of comprehensive bibliometric analysis in this research area. Objective This article aims to present the current status and hot topics of epigenetic research in ADs from a bibliometric perspective, as well as explore the frontier hotspots and trends in epigenetic studies related to ADs. Methods This study collected 1,870 epigenetic records related to autoimmune diseases from the Web of Science Core Collection (WoSCC) database, spanning from 2012 to 2021. Analysis of regions, institutions, journals, authors, and keywords was conducted using CiteSpace, VOSviewer, and the R package "bibliometrix" to predict the latest trends in epigenetic research relevant to autoimmune diseases. Results The number of epigenetic publications related to autoimmune diseases has been increasing annually. The United States has played a major role in this field, contributing over 45.9% of publications and leading in terms of publication volume and citation counts. Central South University emerged as the most active institution, contributing the highest number of publications. Frontiers in Immunology is the most popular journal in this field, publishing the most articles, while the Journal of Autoimmunity is the most co-cited journal. Lu QJ is the most prolific author, and Zhao M is the most frequently co-cited author. "Immunology" serves as a broad representative of epigenetic research in ADs. Hot topics in the field of epigenetic modifications associated with autoimmune diseases include "regulatory T cells (Treg)," "rheumatoid arthritis," "epigenetic regulation," "cAMP-responsive element modulator alpha," "cell-specific enhancer," "genetic susceptibility," and "systemic lupus erythematosus." Furthermore, the study discusses the frontiers and existing issues of epigenetic modifications in the development of autoimmune diseases. Conclusion This study provides a comprehensive overview of the knowledge structure and developmental trends in epigenetic research related to autoimmune diseases over the past 11 years. The research findings summarize and clarify the forefront and future trends in studying the association between epigenetics and autoimmune diseases, serving as a reference for scholars engaged in exploring the relationship between epigenetics and autoimmune diseases .