Objective To investigate the organizational structure, routine management, emergency response, and material reserves related to the prevention and control of infectious diseases in maternal and child health institutions at all levels in Sichuan, and to understand the construction of emerging infectious diseases prevention and control system in maternal and child health institutions throughout the province. Methods We conducted a survey on the current situation of the epidemic prevention and control system in maternal and child health institutions using a self-developed questionnaire, which was conducted in October 2020 and July 2021, respectively. We conducted comparative analysis on the basic situation, the construction of emerging infectious disease prevention and control systems, and the setting and management of fever clinics/rooms of maternal and child health institutions at all levels in Sichuan in 2020 and 2021. Results In 2020, a total of 166 maternal and child health institutions participated in the survey, and 166 questionnaires were collected, including 17 at the provincial and municipal levels and 149 at the county level. In 2021, a total of 182 maternal and child health institutions participated in the survey, and 182 questionnaires were collected, including 17 at the provincial and municipal levels and 165 at the county level. In 2021, all levels of maternal and child health institutions in Sichuan had established epidemic prevention and control leadership groups. Compared with 2020, the construction of the emerging infectious disease prevention and control system in maternal and child health institutions at all levels in Sichuan in 2021 had improved to a certain extent in terms of establishing epidemic prevention and control leadership groups, hospital area three channel management, three-level pre-examination triage, inpatient area allocation, staff management, and patient management (P<0.05). Compared with 2020, fever clinics that met the requirements of three zones and two channels management, fever clinics that met the requirements of closed-loop management, and management of fever clinics/rooms in maternal and child health institutions at all levels in Sichuan in 2021 had improved to a certain extent (P<0.05). Conclusion Through strengthened construction during the epidemic prevention and control period, the construction of the emerging infectious disease prevention and control system in maternal and child health institutions in Sichuan has improved, but still faces continuous challenges in normalized prevention and control.