A method, an apparatus, and a system for detecting Botnet are disclosed. The method for detecting Botnet includes: obtaining an address information about a control host in a Bot sample by using an auto breakout environment; sending a query request message to a traffic analysis device to obtain an address information of a Bot host connected with the control host, in which the query request message carries the address information about the control host; and receiving a query response message returned by the traffic analysis device, in which the query response message carries the address information of the Bot host connected with the control host. The method for detecting Botnet can obtain the Botnet information in real time and construct a topology of the Botnet.