The invention discloses a method and a system for transmitting data between heterogeneous different networks. A plurality of data sources are positioned in the heterogeneous different networks, and each data source generates a position package to be sent to a position base; the position base compares update positions in the position packages to determine whether position label information, address information and the like are re-set up or updated or not and maintain position label indexes; when initial data sources request data to target data sources, the initial data sources firstly generatelabel data packages to be sent to position bases, and the label data package comprises position label information with objective marking as target data sources; the position bases read the objective markings and obtains the address information of the target data sources and the like through the position label indexes; and transparent data flow channels between the initial data sources and the target data sources are set up to carry out data transmission. With the technical scheme of the invention, the data transmission of automatic point to point, point-multipoint, multipoint-point, and multipoint-multipoint without human intervention between a plurality of data sources in the heterogeneous environment of heterogeneous different networks can be realized.