Partial anomalous pulmonary venous drainage (PAPVD) is a common congenital heart disease. If the insertion of an anomalous pulmonary vein (PV) is high into the superior vena cava (SVC), the traditional 1-patch or 2-patch surgical repair might be challenging. Unlike patch procedures, the cavoatrial anastomosis technique (Warden procedure) theoretically reduces complications such as sinus node dysfunction and venous obstruction. We investigate outcomes of the Warden procedure (WP) at a single institution. A total of 67 patients (42 males and 25 females) with PAPVD who underwent the WP between January 2011 and December 2018 were consecutively enrolled. The median age was 2.8 years (3–61 years old). 52 cases were younger than 18 years old. perioperative and follow-up clinical data were collected. In addition, we selected possible risk factors (a total of 18 risk factors) of SVC stenosis or obstruction. Univariate and multivariate analyses were conducted to confirm the independent risk factors. The average Cardiopulmonary bypass (CPB) time was 132.3 ± 46.3 min, and the aortic cross-clamp time was 85.2 ± 35.7 min. One patient died postoperatively in hospital. The mean follow-up time of the remaining patients (n = 66) was 15.8 ± 14.5 months (3–64 months). No abnormal cardiac function or sinus node dysfunction cases were identified during the follow-up. Of the survival patients, no venous obstruction was presented before the discharge. Numbers of patients identified with mild PV and SVC stenosis were 1 (1.5%) and 7 (10.6%, 4 of them turned negative eventually) at discharge. At the last follow-up, no PV obstruction was identified, whereas, 4 cases (6%) had SVC obstruction. Numbers of PV and SVC stenosis cases were 3 (4.5%) and 8 (12%). Univariate and multivariate analyses showed that only the diameter of SVC less than 10 mm was an independent risk factor for SVC stenosis or obstruction at the last follow-up. Warden procedure can effectively treat PAPVD (anomalous drainages into SVC), with satisfactory early and mid-term postoperative results. Different modifications of the Warden procedure may be selected according to the anatomic characteristics. The diameter of SVC less than 10 mm predicts SVC stenosis or obstruction after Warden procedure.