A prospective, observational single-center study was carried out. Pediatric patients undergoing congenital heart defect surgery were evaluated before, during, and after surgery. At each time point, sublingual microcirculation and clinical parameters were assessed, along with analytical variables. Twenty-four patients were included. All microcirculatory parameters worsened during cardiopulmonary bypass and returned to baseline values after surgery (p ≤ 0.001). In the intraoperative evaluation, body temperature correlated with perfused small vessel density (p = 0.014), proportion of perfused small vessels (p < 0.001), small vessel microvascular flow index (p = 0.003), and small vessel heterogeneity index (p < 0.002). Patients with cyanotic disease exhibited higher small vessel density (p < 0.008) and higher density of perfused small vessels (p < 0.022) at baseline, and a lower microvascular flow index (p = 0.022) and higher heterogeneity (p = 0.026) in the intraoperative phase. Children with congenital heart disease exhibited decreased vascular density and microvascular blood flow and increased heterogeneity during cardiopulmonary bypass. All these parameters returned to baseline values after surgery.