This study identified a potential TF–miRNA–mRNA network, including the key regulons of two TFs (TP53 and TWIST1), four miRNAs (has-miR-107, has-miR-10b-5p, has-miR-659-3p, and has-miR-371a-5p), and four mRNAs (PIM3, CHUK, F2RL1, and CA1), that can help enrich the connotation of HSCR pathogenesis and diagnosis and provide new horizons for treatment. Here, TF is linked to Hirschsprung disease.