Alpha-thalassemia occurs with high frenquency in China. Four common α-globin gene deletion mutations (-SEA, -α3.7, and -α4.2, Haemoglobin Constant Spring (CS) mutation) were identified in Chinese patients. Individuals with alpha-thalassemia syndrome are more often of children. However report on endocrinal complications in children with alpha thalassemia in China are still absent. The present study aimed to investigate the impact of genotype on endocrinal complications in Chinese children. Association analysis between genotype and endocrinal compliaction development was conducted on 200 patients with 200 healthy controls. Hypogonadism was found to be the most prominent endocrinal complications (84.0%) leading to the growth retardation, hypogonadism, diabetes mellitus, hypothyroidism and hypoparathyroidism whose incidence were significantly higher in pateints. (αCSα/-SEA) was the main genotype of Alpha thalassemia identified in the patients (37.5%), and patients with the (-α4.2/-SEA) genotype had a higher prevalence of hypogonadism, diabetes mellitus and hypoparathyroidism (P = 0.001, P = 0.001, P < 0.001, respectively).