A method and a system for encrypting a data stream are provided. The method includes receiving a multimedia data stream including multiple data elements; dividing the multimedia data stream into M data sub-streams based on sequence of the multiple data elements in the multimedia data stream, where the M data sub-streams follow a synchronous clock period which is M times of a clock period of the multimedia data stream, where M is a positive integer greater than 1; and generating a key at a predetermined time interval with a new pipeline algorithm, and encrypting the data elements in the M data sub-streams with the key and the complicated control logic, and the predetermined time interval is N times of the clock period of the M data sub-streams, where N is a positive integer.