If you were restricted to a 1 mile stretch of road, where you could only start at one end and finish at the other, the MTB would be more exercise because it takes more effort per mile to use.
I think the speed of the road bike may be clouding your perception, either that or you have a road bike that is less efficient than your MTB. In other words, it could very well be that your MTB is lighter and faster than your road bike.