Originally Posted by Looigi

A road bike will go up hill better because it lighter, has less rolling resistance, and is stiffer in pedaling. Does your mountain bike have suspension? Suspension absorbs not only energy of impacts but also the energy of rider, especially rear suspension. Locking it out helps. Differing riding position between the two bikes can have an effect on your pedaling efficiency too. Saddle height and setback being the most important when your seated.