A work vehicle includes a work implement. A control system for the work vehicle includes an operating device and a controller. The operating device outputs an operation signal indicative of an operation by an operator. The controller communicates with the operating device and controls the work implement. The controller determines a first target design topography. The controller generates a command signal to operate a work implement in accordance with the first target design topography. The controller obtains a displacement amount of the work implement with respect to the first target design topography upon receiving the operation signal indicative of the operation of the work implement during work in accordance with the first target design topography. The controller determines a second target design topography based on the displacement amount. The controller generates a command signal to operate the work implement in accordance with the second target design topography.