Objective To explore the spatial distribution characteristics of birth defects in China and to provide scientific evidences for effective prevention and control of birth defects. Methods The database of incidence of birth defects from 1996 to 2012 was established. The ordinary Kriging interpolation was adopted to plot the map of incidence of birth defects in China. The spatial autocorrelation analysis, trend surface analysis, and spatial regression analysis were conducted for the incidence of birth defects. Results Global spatial autocorrelation analysis showed that the spatial aggregation of birth defects in China existed during 1996-2004 (I=0.226, P=0.000 6) and 2005-2012 (I=0.283, P=0.000 03). Local spatial autocorrelation analysis showed that Guangdong, Guangxi, and Fujian were “positive hotspot” regions and Heilongjiang, Jilin, and Liaoning were “negative hotspot” regions. Trend surface analysis showed that the incidence of birth defects increased first and then decreased from west to east and gradually increased from north to south. Spatial regression analysis showed that with the increase of latitude, the incidence of birth defects decreased. Conclusion The incidence of birth defects in China is of significantly geographical distribution. Different prevention and control measures should be established for different regions.