Background Anal abscess is an important complication of anal fissure (AF), whereas interleukin‐6R (IL‐6R) has been implicated in the development of abscess. In this study, we aimed to explore the possible molecular mechanisms underlying the regulatory effects of miRNAs on IL‐6R and other inflammatory factors related to the induction of anal abscess in AF. Methods Bioinformatics analysis, luciferase assay, real‐time polymerase chain reaction, and Western blot analysis were performed to identify the possible regulatory relationships between IL‐6R and miR‐124/miR‐125a by comparing the differentiated expression of miR‐125a, miR‐124, tumor necrosis factor‐α (TNF‐α), interferon‐γ (IFN‐γ), and IL‐4 among different groups of AF patients. Results IL‐6R messenger RNA (mRNA) was identified as a target gene of miR‐124 because the luciferase activity in cells cotransfected with wild‐type IL‐6R and miR‐124 mimics was significantly reduced. In addition, the expression of IL‐6R mRNA and protein was significantly inhibited in the presence of miR‐124 or an IL‐6R inhibitor, confirming the presence of a negative regulatory relationship between miR‐124 and IL‐6R. Moreover, miR‐124 and inflammatory factors were differentially expressed in AF patients carrying different genotypes of rs531564 polymorphism. Conclusions miR‐124 and inflammatory factors TNF‐α, IFN‐γ, and IL‐4 may be used as indicators of anal abscess development in AF patients. In addition, miR‐124 polymorphism rs531564 is involved with the pathogenesis of anal abscess in AF patients, and the presence of rs531564 may increase the incidence of anal abscess via upregulating the expression of IL‐6R, TNF‐α, IFN‐γ, and IL‐4.