This study investigated the morphologic changes of portal cavernoma in children with extrahepatic portal venous obstruction and explored the relationship with prognosis. From February 2008 to October 2017, there were 107 patients with cavernous transformation of the portal vein admitted to our hospital. Rex shunts were performed in 99 cases, Warren shunts in 7 cases, and laparoscopic splenic vessel ligation in 1 case. Intraoperative superior mesenteric venography was used to determine the structure of the portal venous system. According to the morphologic features of the portal vein shown by portal venography, groups were assigned as follows: patients with the cotton form of portal cavernoma; patients with visible collateral veins of portal cavernoma; patients with and without a visible left gastric vein; and patients with and without a clearly visible intrahepatic portal vein. The preoperative and postoperative portal pressure, preoperative incidence of esophageal varices, time at onset, incidence of postoperative rebleeding, preoperative and postoperative size of the spleen, and age at time of operation were compared between these groups. The preoperative incidence of esophageal varices, time at onset, postoperative size of spleen, and age at time of operation were significantly lower in the group with the cotton form than in those with visible collateral veins (P < .05). There was a significant correlation between the visible left gastric vein and esophageal varices (P = .002). The time at onset, preoperative and postoperative size of the spleen, and age at time of operation were markedly lower in the group with a good visible intrahepatic portal vein than in those without a clearly visible intrahepatic portal vein (P < .05). The visible left gastric vein was notably associated with the performance of a gastroportal shunt (P = .000), and the group with a visible left gastric vein had a higher ratio of children undergoing a gastroportal shunt. The cotton form, an early-stage manifestation of cavernous transformation of the portal vein, typically occurs in younger children with a shorter time to onset. Children with the cotton form of portal cavernoma typically have a better prognosis after Rex shunt.