Purpose Severe acute pancreatitis (SAP) is a life-threatening inflammatory syndrome of the pancreas. This study aimed to analyze the clinical significance of runt-associated transcription factor 3 ( RUNX3 ) and fibroblast growth factor receptor 2 ( FGFR2 ) expression alterations in SAP. Methods This study included 18 SAP patients in Wuzhong People’s Hospital from November 2019 to December 2021 and 18 healthy controls. RUNX3 and FGFR2 expression levels were determined by RT-quantitative PCR. Correlations between RUNX3 / FGFR2 and sex, age, etiology, CRP, procalcitonin, AST, LDH, BUN, Acute Physiology and Chronic Health Evaluation II (APACHE II), Ranson score, Bedside Index for Severity in Acute Pancreatitis (BISAP) score, sequential organ failure assessment (SOFA), and modified computed tomography severity index (MCTSI) score were analyzed. Diagnostic values of RUNX3 and FGFR2 in SAP were analyzed using the receiver-operating characteristic curve. The binding of RUNX3 to FGFR2 was analyzed by chromatin immunoprecipitation. Results RUNX3 and FGFR2 were downregulated in peripheral blood of SAP patients. RUNX3 and FGFR2 were negatively correlated with CRP, procalcitonin, AST, LDH, BUN, APACHE II score, Ranson score, BISAP score, SOFA score, and MCTSI score. Sensitivity and specificity of RUNX3 level of <0.9650 for SAP diagnosis were 88.89% and 72.22%, respectively. Sensitivity and specificity of FGFR2 level of <0.8950 for SAP diagnosis were 66.67% and 83.33%, respectively. RUNX3 was enriched in the FGFR2 promoter and was positively correlated with FGFR2 . Conclusion RUNX3 and FGFR2 were downregulated in peripheral blood of SAP patients and served as candidate biomarkers for SAP diagnosis. RUNX3 bound to the FGFR2 promoter to promote FGFR2 transcription.