This invention discloses a method and system for implementing transparent multi-buffering in multi-GPU graphics subsystems. The purpose of multi-buffering is to reduce GPU idle time. In one example, after rendering a first image by a first GPU in a back buffer, the first image is displayed by flipping to the back buffer. After that, the front buffer and back buffer are exchanged, and then shifting the back buffer and internal buffers in a predetermined sequence. A second image is rendered to current back buffer by a second GPU. The second image is displayed by flipping to a current back buffer. After that, the front buffer and back buffer are exchanged again, and shifting the back buffer and internal buffers again.