A system and a method for replicating data among heterogeneous databases are disclosed. The system comprises: an initialization module for creating and initializing at least one shared memory, at least one message queue and at least one semaphore in a computer; a source data processing module including a data reader, a data adapter and a data loader; a target data replication module for replicating the data in the shared memory to at least one target database according to the messages in the message queue; and a cleaning module for releasing the shared memory after the replication has been completed. The method comprises the steps of: creating and initializing the shared memory, the message queue and the semaphore in the computer; reading data from at least one source database, then converting the data into target data to be stored in at least one target database, and loading the target data in the shared memory; replicating the target data in the shared memory to the at least one target database according to the messages in the message queue; and releasing the shared memory after the replication has been completed.