The invention discloses a method and a system for auditing open ports of hosts. The method comprises the following steps of performing scanning configuration on hosts in one or more networks, and setting scanning modes; scanning the hosts in one or more networks according to the scanning configuration to obtain corresponding scanning results; collecting the scanning results, and importing the scanning results into a database; analyzing and processing the scanning results, acquiring scanning information and generating a scanning information report, wherein the scanning modes include the rapid scanning mode, the accurate scanning mode and the comprehensive scanning mode. The scanning modes of the open ports are set to be rapid scanning, accurate scanning or comprehensive scanning, and thereby the hosts in one or more networks are scanned according to the different scanning modes, multiple selections are provided, and the method for auditing the open ports is extended. The problems that the existing method is simplex, poor in flexibility and has certain restriction when being used for auditing a large number of open ports of the hosts in the network are effectively solved.