The present disclosure relates to a focus tracking system and method. The system comprises: a primary camera comprising a first focus adjustable lens and a first focus adjusting servo motor driving the first focus adjustable lens to perform focus adjusting; a secondary camera comprising a second focus adjustable lens and a second focus adjusting servo motor driving the second focus adjustable lens to perform focus adjusting, coded aperture is installed inside the second focus adjustable lens, the secondary and primary camera have equivalent optical parameters; a synchronization system performing frame level synchronization between images of the primary and secondary camera to obtain frame-level synchronized primary and secondary camera images; a focus control system calculating out-of-focus offset utilizing coded patterns of the coded aperture and out-of-focus images in the frame-level synchronized secondary camera images, sending focus adjusting signals to the first and second focus adjusting servo motor based on the out-of-focus offset.