The present invention relates to a method of controlling a variable damper in a vehicle wherein a rear-wheel variable damper can be controlled by estimating a vertical acceleration value of a rear wheel based on the fact that there is a certain time delay in a wheel motion between front and rear wheels due to the wheelbase and vehicle speed. To this end, the method of the present invention comprises the steps of (a) detecting vehicle body accelerations other than a desired vehicle body acceleration of a vehicle body; (b) calculating the desired vehicle body acceleration based on the other detected vehicle body accelerations according to a geometric rule; (c) calculating vehicle body vertical velocities by filtering the vehicle body accelerations to eliminate DC offsets therefrom and integrating the filtered accelerations; (d) detecting accelerations of front right/left vehicle wheels; (e) calculating front wheel vertical velocities by filtering the detected accelerations of the front right/left wheels to eliminate DC offsets therefrom and integrating the filtered accelerations, and then calculating accelerations of rear wheels by time delaying the accelerations of the front wheels by a time interval taken while a road input to the front wheel is delivered to the rear wheel at a vehicle speed; and (f) calculating damper velocities based on the calculated vehicle body vertical velocities and the calculated vehicle wheel vertical velocities. Accordingly, the Sky-hook determination can be more accurately made. Further, since it is not necessary to use all the four sensors, the number of parts of vehicles can be reduced when mass-producing the vehicles. Consequently, the selling prices for finished vehicles can be lowered, and thus, an unnecessary economical burden cannot be imposed on the consumers.