The invention provides a ventilation control method and system for hospitals. The method comprises the following steps that a central data extraction and operation processing platform extracts hourly outpatient visit N from a hospital out-patient registration information management system, and obtains hourly outpatient visits of sub spaces according to the hourly outpatient visit N; the relation model between the hourly outpatient visits and the hourly human traffics of the sub spaces is established finally, and the hourly human traffics M of the sub spaces of a hospital are obtained through calculation; the central data extraction and operation processing platform extracts local outdoor hourly air temperature parameters dynamically from a public meteorology database; a fresh air control strategy predicating model based on indoor air quality and energy conservation is established according to the hourly human traffics of the sub spaces and the temperature parameters; and a fresh air controller controls the rotation speed of a fresh air ventilator according to the fresh air control strategy, and supplies fresh air into a room in real time properly. The ventilation control method and system for hospitals ensure the indoor air quality of hospitals and save energy.