Birth defects (BD) is a big public health issue in Guangxi Zhuang Autonomous Region of China. The overall prevalence of BD in Guangxi is about 1% and higher than most other provinces of China. However, the geographical clustering variations in BD of Guangxi has not been described. Therefore, the aim of this study was to explore and detect the spatial clustering patterns of BD prevalence across a well-defined geographic space. The data were obtained from Guangxi birth defects monitoring network (GXBDMN) from 2016 to 2020, which collected socio-demographic and clinical information from perinatal infants between 28 weeks of gestation and 7 days postnatal. The spatial autocorrelation analysis and hot spot analysis will be used to explore the geographical clustering of BD prevalence in 70 counties and 41 districts of Guangxi in this study. A total of 44,418 perinatal infants were born with BD from 2016 to 2020. The overall prevalence of BD was 122.47/10,000 [95% confidence interval (CI): 121.34-123.60/10,000]. The local indicators of spatial association (LISA) statistic and Gi* statistic showed that the spatial clustering patterns of BD prevalence changed over time, and the largest High-High clustering area and hot spot area were both identified in the city of Nanning. Therefore, the spatial clustering patterns of BD prevalence in Guangxi is very significant. Spatial cluster analysis can provide reliable and accurate spatial distribution patterns in BD control and prevention.