Background: It becomes increasingly important to measure the health-related quality of life (HRQoL) of rare diseases in children and adolescents in recent decades. Much attention has been paid to investigate the HROoL of one specific rare disease by self-report in previous studies. This study aimed to evaluate and compare the HROoL of 11 rare diseases in Chinese children by parent proxy-report, to explore the factors associated with HROoL of patients and to know the problems of most concern.Methods: A total of 651 children aged from 2 to 18 were enrolled from the Children’s Hospital Affiliated Zhejiang University in 2018. Their parents completed the parent proxy-reports version of the Pediatric Quality of Life InventoryTM 4.0 (PedsQLTM). Independent samples t-test, one-way ANOVA, or Kruskal-Wallis H test was used to compare HROoL scores between groups. Multilevel linear regression models with random intercept were applied to analyze the relationship between socioeconomic variables and both the total score and sub-domain scores.Results: The total PedsQL scores of Patent ductus arteriosus, Infantile agranulocytosis, Autoimmune thrombocytopenia, Polysyndactyly, Hirschsprung disease, Cleft lip and palate, Tetralogy of fallot, Myasthenia gravis, Guillain-barre syndrome, Glycogen storage disease, and Langerhans cell histiocytosis children were 79.65±5.46, 95.88±3.48, 71.39±3.27, 91.77±6.35, 76.18±6.92, 96.33±4.22, 77.85±8.90, 95.99±3.31, 85.77±4.56, 82.97±4.13 and 77.6±5.15, respectively. Age was significantly associated with physical functioning, school functioning, and psychosocial health score. Gender and The household registration place was significantly associated with the overall score. The most urgent desire of patients was reducing the overall medical costs.Conclusions: These data show that Patent ductus arteriosus scores lowest in physical functioning, Autoimmune thrombocytopenia (ITP) ranks the lowest in the emotional functioning score, social functioning score, school functioning score, psychosocial health score, and total score. Incentive policies should be further taken to improve orphan drug availability and reduce the financial burden of rare diseases.