In a method and system for 3D comb synchronization and alignment of standard and non-standard video signals, a coarse synchronization is performed on a bottom frame, a current frame, and a top frame based on a bottom frame field count. The current frame is assigned the frame transferred immediately prior to a bottom frame whereas the top frame is assigned the frame transferred two frames. A current frame window signal and a top frame window signal may be used to lock the current frame and the top frame to a bottom frame vertical sync signal. After coarse synchronization, the video frames are finely aligned by correlating a phase difference between the subcarrier signals in each frame and modifying the phase difference until the correlation results in a specified phase locked value range. This method and system may facilitate the handling of video stream switching and non-standard data streams.