A 4-year-old boy was diagnosed with pulmonary artery atresia accompanied by ventricular septal defect, branch pulmonary artery hypoplasia, and collateral vessel formation. He was scheduled to undergo pulmonary artery unifocalization procedures under general anesthesia. Refractory hypotension, hypoxemia, and metabolic acidosis occurred during the surgery, and cardiopulmonary bypass (CPB) support was needed to help finish unifocalization procedures. Pulmonary artery unifocalization procedures are often complex and very lengthy. Collateral vessel ligation may significantly reduce pulmonary blood flow and blood loss, leading to hemodynamic instability and arrhythmias. Anesthetic management poses a considerable challenge to anesthesiologists. The keys to anesthetic management during pulmonary artery unifocalization procedures include maintaining stable hemodynamics, ensuring sufficient organ perfusion, and keeping homeostasis.