Abstract: To analyze the geographical and spatial distribution characteristics of physical morphology of 3-6-year-old children in China, and to explore the impact of natural environmental factors on the development of children’s physical morphology． Using GIS spatial analysis method, this study examined 23,072 3-6-year-old children, focusing on the north-south differences, regional characteristics, spatial correlation, cold/hot spot distribution, and correlations with natural environmental factors of physical morphology indicators such as height, weight, BMI, chest circumference, shoulder width, and Kaup index． (1) Children’s physical morphology showed characteristics of age-related increase, regional differentiation, and gender differences． (2) In terms of spatial correlation, the standardized Z-values of children’s weight and Kaup index were greater than 1.65, indicating a significant positive spatial correlation (i.e., high values adjacent to high values and low values adjacent to low values) in these two indicators． (3) From the perspective of spatial cold/hot spot distribution, the regional distribution of children’s weight and Kaup index showed a pattern of "higher in the north and lower in the south", with an overall increasing trend from the southwest to the northeast． Both high-value and low-value areas presented agglomerated distributions． Hot spot areas were concentrated in North China, showing a patchy distribution; cold spot areas were concentrated in Central South China and Southwest China, showing a clumped distribution． (4) Annual averaged relative humidity, annual averaged temperature, and latitude were critical natural environmental factors affecting children’s physical morphology． Specifically, the higher the latitude, the greater the children’s weight and Kaup index． Conclusions: The physical morphology of 3-6-year-old children in China shows significant regional differences between the north and south, east and west, and among the six major administrative regions． There are also spatial correlations and regional differentiation in spatial cold/hot spots． Annual averaged relative humidity, annual averaged temperature, and latitude are important natural environmental factors affecting children’s physical morphology．