Objective To understand the situation of students' absence due to illness and the monitoring of early warning system in Pukou District,and to provide scientific basis for the prevention and control of infectious diseases in schools. Methods The descriptive epidemiological method was used to analyze the monitoring data of absence due to illness in all primary and secondary schools and kindergartens in Pukou District of Nanjing City from 2019 to 2020, and the monitoring results of early warning system were analyzed. Results In the 2019-2020 school year, the average number of days absent from school due to illness among primary and secondary school students in Pukou District was 1.39, and the absentee rate was 0.36%. The average number of days absent from school due to illness was 1.42 for nursery school students, and the absentee rate was 0.55%. The symptom composition showed that fever was the main reason for primary and secondary school students absent from school due to illness, and cough was the main reason for kindergarten students. The disease composition showed that cold was the main reason for primary and secondary school students absent from school due to illness, as well as the main reason for kindergarten students. The absence of primary and secondary school students due to illness showed two peaks in December and May to June, while that of kindergarten students in November to December and June. The monitoring results of the absence early warning system showed that the main disease warning for primary and secondary school students and kindergarten students was cold, the main reason for early warning of symptoms of primary and middle school students was fever, and the main reason for early warning of symptoms for kindergarten students was cough. Conclusions Monitoring the absence of students due to illness was an important measure to advance the prevention and control of infectious diseases. Through the absence warning system, early detection, early reporting, and early disposal of school infectious diseases can be achieved. It can effectively reduce the occurrence of clusters of infectious diseases in schools and public health emergencies. The occurrence of public health emergencies is particularly important under the situation of normalized prevention and control of the new crown pneumonia epidemic, which is particularly important under the situation of normalized prevention and control of the COVID-19.