Thalassemia is a common monogenic disease in southwestern China, especially in Guizhou province. In this study, 18 309 neonates were examined for thalassemia. The thalassemia carrier rate was 12.90%, which is associated with geographical regions, with carrier frequencies significantly differing between regions (p < 0.0001). The carrier rates for α‐thalassemia and β‐thalassemia were 8.91% and 3.36%, respectively. There are 22 genotypes identified among 1632 α‐thalassemia cases, and 18 genotypes detected among 615 β‐thalassemia cases. The birthrates of individuals with intermediate thalassemia and β‐thalassemia major were 0.153% and 0.055%, respectively. Methodologically, NGS‐Gap‐PCR is superior to traditional detection methods, with 65 more cases detected by NGS‐Gap‐PCR. Since thalassemia‐rich genotypes were highly prevalent in this region, early detection of thalassemia carriers would be meaningful for genetic counseling and prevention/treatment of thalassemia. NGS‐Gap‐PCR provides a powerful tool for neonate genetic testing and clinical diagnosis of thalassemia, especially in high‐prevalence regions.