(1) Background: Enterobius vermicularis infection causes a significant health burden in children. The infection occurs throughout the country and remains a serious public concern in China. Therefore, it is necessary to know the situation of E. vermicularis infection, to provide a scientific basis for the disease control and the optimum conditions for children’s growth. (2) Methods: Descriptive epidemiological analysis was implemented to demonstrate the status and changing trend of E. vermicularis infection from 2016 to 2020, while the spatial distribution characteristics and spatial-temporal clustering were illuminated by spatial autocorrelation analysis and spatio-temporal scanning analysis. (3) Results: The infection of E. vermicularis showed a fluctuating downward trend with a decline of 32.00% in 2020 compared to that in 2016 and was concentrated in central and southern China. There was no significant difference in infection rate between boys and girls, while the high infection rate was presented in 4-, 5- and 6- year-old children. The hotspots and spatial clustering areas were mainly concentrated in southern China. (4) Conclusions: From 2016 to 2020, the infection rate of E. vermicularis in children aged 3 to 9 years in China demonstrated a declining trend, and its distribution showed spatial clustering, mainly in southern China. Therefore, it is necessary to strengthen surveillance and implement control measures in combination with health education and environmental improvement.