If there is negative height, what is its implication? Or meaning?

Really depends on the context.
Could mean below sea level, which is fine in a car, but not so good in an aeroplane..

In physics we typically think of an object's height as a positive number if it is higher than some reference point and negative if it's lower. For example: the height of a 3 story bulding above the ground may be about +50 feet, but the height of its basement floor would be about -15 feet. In this way you can calculate that the difference in height between the roof and basement floor is 50 - (-15) = 65 feet.