Objective To investigate the effect of new type ultrafiltration technique in preventing and relieving the main organ injury that may follow open heart surgery with cardiopulmonary bypass (CPB),and improve the operative effects and decrease the postoperative complications. Methods Thirty patients with congenital heart diseases were randomly divided into two groups. Modified ultrafiltration group: modified ultrafiltration was used after CPB; new type ultrafiltration group: new type ultrafiltration technique was used throughout CPB. The serum concentrations of nflammatory mediators,hematocrit,serum albumin concentrations, pulmonary function, operative duration time and main organ function parameters were measured in both groups. Results Ultrafiltration time after CPB in new type ultrafiltration group was significantly shorted as compared with modified ultrafiltration group（6.35±1.28 min vs. 12.45±4.52 min，P=0.000）; serum concentrations of interleukin6(IL-6)and tumor necrosis factor α(TNF-α) after CPB were significantly decreased as compared with modified ultrafiltration group（292.84±58.23 μg/L vs. 383.79±66.24 μg/L,P=0.000; 13.32±2.31 μg/L vs. 16.41±2.65 μg/L,P=0.000）; the hematocrit and serum albumin concentrations at the ten minutes after CPB were increased as compared with modified ultrafiltration group (0.39±0.04 vs. 0.35±0.03,P=0.003; 38.32±4.26 g/L vs. 34.04±2.83 g/L, P=0.003); the mechanical ventilation support time and ICU time after operation was shorted as compared with modified ultrafiltration group (Plt;0.05); main organ function was improved as compared with the modified ultrafiltration group. Conclusion The clinical application of new type ultrafiltration throughout CPB can effectively exclude some harmful inflammatory mediators, concentrate blood,short operation time,attenuate the main organ edema and injury.