Objective To explore the situation and countermeasures of comprehensive prevention and control of birth defects in Nanning. Methods The situation of comprehensive prevention and control of birth defects in Nanning was investigated and analyzed, and corresponding countermeasures were put out forward by comprehensively employing research methods such as literature data analysis and field research. Results (1) There was a statistically significant difference in the incidence rate of perinatal birth defect in different regions of Nanning from 2020 to 2022 (P<0.05). The incidence rate of perinatal birth defects in the whole city of Nanning and Hengzhou demonstrated an upward trend with the increase of years (P<0.05), therein the incidence rate of perinatal birth defects in Xixiangtang District, Shanglin County, and Mashan County was higher than the average level in the whole city (P<0.05). Although there was no statistically significant difference in the incidence rate of perinatal birth defects in Xixiangtang District, Jiangnan District, Wuming District, and Mashan County from 2020 to 2022, the incidence rate of perinatal birth defects showed an upward trend with the increase of years. (2) From 2020 to 2022, the top five incidence rate of perinatal birth defects in Nanning were congenital heart disease, polydactyly, hydrocele of tunica vaginalis, syndactyly, and talipes equinovarus, successively. The morbidity of congenital heart disease was higher than that of other birth defects (P<0.05). The overall incidence rate of birth defects rebounded slightly in 2022 compared with 2021 in Nanning (P<0.05). (3) The incidence rate of severe fatal and disability of birth defects of perinatal infants in the whole city of Nanning depicted an upward trend with increase of years from 2020 to 2022 (P<0.05). From 2020 to 2022, the intervention rate of severe fatal and disability of birth defects in perinatal infants <28 weeks was more than 90% in the whole city of Nanning. However, the intervention rate in Xingning District, Xixiangtang District, Yongning District, Hengzhou, and Shanglin County did not reach 90% by 2022; moreover, in Nanning, the top three regions in terms of the birth rate of severe fatal and disability of birth defects were successively Qingxiu District, Wuming District, and Binyang County in 2020, and were successively Liangqing District, Binyang County, and Wuming District in 2021, and Hengzhou, Wuming District, and Xixiangtang District in 2022. Conclusion Since 2020, the comprehensive prevention and control of birth defects in Nanning has achieved initial results, which has been significantly effective in the statistics and reporting of birth defects, and timely intervention, greatly reducing the occurrence of severe fatal and disability of perinatal birth defects. However, there are still some problems in the prevention and control of birth defects in Nanning, such as lack of medical resources, insufficient public awareness, and to be improved policy system. It is suggested that the joint prevention and control should be carried out from multi⁃angle, multi⁃level and multi⁃center to effectively control the birth rate of severe fatal and disability of birth defects of perinatal infants in Nanning, so as to further improve the quality of the city's birth population.