The present disclosure provides a program integrity monitoring and contingency management system and method. The system includes a monitoring-notifying module and a contingency management module. The monitoring-notifying module includes a management unit configuring an exclusion profile and a program integrity monitoring profile, a setup unit establishing a file integrity baseline list according to the program integrity monitoring profile, a notifying unit, and an integrity comparison unit comparing the exclusion profile and the file integrity baseline list with the program integrity file, and generating an abnormality warning when the comparison result is abnormal and instructing the notifying unit to report the same. The contingency management module includes an evidence-collecting unit collecting and storing the program integrity file upon generation of an abnormality warning, and a software malicious program detection unit comparing the program integrity file with virus signatures in a database to determine whether the program integrity file is a software malicious program.