Embodiments of the present disclosure provide a code stream processing method and system, and a multipoint control unit. The code stream processing method includes: obtaining code stream information of each site, and type attribute information of a target site; determining a site type of the target site according to the type attribute information, searching a code stream processing policy file to obtain a code stream output policy corresponding to the site type of the target site; and according to code stream output policy, using the code stream information of each site to generate a code stream of the target site and sending it to the target site to present it in the target site.