Background: Thalassemia is an inherited hemolytic disease, the complications and sequelae of which have posed a huge impact on both patients and society. But limited studies have investigated the molecular characterization of alpha- and beta-thalassemia in children from Guizhou, China. Methods: Between January 2019 and December 2022, a total of 3301 children, aged 6 months to 18 years, suspected of having thalassemia underwent molecular analysis. Results: Out of the total sample, 824 (25%) children were found to carry thalassemia mutations. The carrier rates of alpha-thalassemia, beta-thalassemia, and alpha + beta-thalassemia were determined as 8.1%, 15.6%, and 1.3%, respectively. Approximately 96.5% of the alpha-thalassemia gene mutations were --SEA (51%), alpha alpha CS (20.9%), -alpha 3.7 (19.6%), and -alpha 4.2 (5.0%). The most prevalent mutations of beta-thalassemia were beta CD17(A>T) (41.5%), beta CD41-42(-TTCT) (37.7%), and beta IVS-II-654(C>T) (11.3%). Additionally, we identified rare cases, including one case with alpha alpha Hb Nunobiki/alpha alpha, two cases with triplicated alpha-thalassemia (one case with alpha alpha alpha/alpha alpha alpha and beta CD41-42/beta N and the other with alpha alpha alpha-3.7/alpha alpha and beta E CD26/beta N), and also one case with alpha Q-Thailand alpha/-alpha 4.2 and beta CD41-42/beta N. Conclusions: Our study findings provide important insights into the heterogeneity of thalassemia carrier rates and molecular profiles among children in the Guizhou region. The findings support the development of prevention strategies to reduce the incidence of severe thalassemia in the future.