A system variably controls braking energy regeneration in a vehicle by reflecting a compensation torque depending on a difference in deceleration based on a road gradient when the vehicle travels over a downhill section or an uphill section of a road. The system includes a longitudinal sensor to receive the road gradient and compare the road gradient to a specific grade, and then compensate for the road gradient using a grade resistance value and a deceleration based value depending on a difference between deceleration manually set by a driver using a paddle shift and an actual vehicle deceleration. The system may include a controller to output a coasting torque as a correction torque that is a sum of the grade resistance value and the deceleration based value.