Background The aim of the present study was to summarize the clinical characteristics of in children aged under 3 years and analyze the related factors affecting the prognosis. Methods The clinical data of 316 children aged under 3 years (192 males and 124 females) who were admitted to Beijing Tongren Hospital with a pathological diagnosis of HB between May 2005 and May 2019 were analyzed retrospectively. The factors influencing the therapeutic effects on and survival of HB in children with HB were analyzed. Results (1) The median age of the enrolled patients was 1.45 years. The most common initial symptom was an abdominal mass (69.0%). The average serum alpha-fetoprotein (AFP) level and platelet count at the initial visit were (97,406.5 +/- 5022.8) ng/mL and (418 +/- 206) x 10(9)/L, respectively. The epithelial type was the main pathological type (51.9%). According to the PRETEXT preoperative typing system, the most common stage was stage III (57.0%), whereas according to the postoperative Evans staging system, the most common stage was stage IV (41.8%). At the initial visit, 62 cases (19.6%) had vascular invasion, 52 cases (16.5%) had extrahepatic tumor extension, and 20 cases (6.3%) had tumor rupture. Distant metastasis occurred in 132 cases, and the most common metastatic site was the lung (80.3%). The incidence in East China was relatively high (35.4%). (2) The children were followed up until May 2020 (the median follow-up duration was 62 months). It was found that 194 patients had complete remission and 62 had partial remission. The Kaplan-Meier survival analysis showed that the overall survival was 95.3, 88.2, and 79.8% at 1 year, 3 years, and 5 years, respectively, and the event-free survival was 91.1, 83.2, and 75.1%, respectively. The Cox regression analysis showed that AFP level, platelet count, PRETEXT IV, vascular invasion, and distant metastasis at the initial visit were independent risk factors for the prognosis of children with HB (p < 0.05 in all). Conclusion The prognosis of HB was correlated with the AFP level, platelet count, PRETEXT staging, vascular invasion, and distant metastasis at initial diagnosis.