Comprehensive data regarding the epidemiology and prevalence of thalassemia in mainland China are lacking. To assess the prevalence of thalassemia, we performed a meta-analysis including 16 articles published from 1981 to 2015. The overall prevalence of α-thalassemia, β-thalassemia and α + β-thalassemia was 7.88%, 2.21% and 0.48%, respectively. Trends in thalassemia prevalence in mainland China were not steady; a prevalence map based on a geographic information system (GIS) showed that the geographic distribution of thalassemia was highest in the south of China and decreased from south to north. Additionally, the most common α- and β-globin gene mutation was --SEA and CD41/42, respectively. The current study provides valuable information regarding epidemiology and intervention and supports the planning, implementation and management of prevention programmes for public health.