A method and a system for generating queue based applications dependencies in virtual machines are provided. The method includes the following steps. At least one transmitting message transmitted via at least one enterprise service bus by a plurality of application programs is intercepted. The at least one transmitting message includes at least one request message. The at least one request message is obtained by filtering the at least one transmitting message. A client and a server of each of the at least one request message are obtained. A checksum of each of the at least one request message is calculated to obtain a message identification of each of the at least one request message. The client, the server and the message identification of each of the at least one request message are recorded in a dependencies table.