A control system for a work vehicle includes a controller. The controller determines a work zone at a work site. The controller determines a target design topography at least partially positioned below an actual topography at the work site. The controller specifies a non-work zone. The non-work zone is a portion in which the actual topography is positioned below the target design topography in the work zone. The controller modifies the work zone based on the non-work zone. The controller generates a command signal to operate a work implement of the work vehicle according to the modified work zone and the target design topography.