Most of Genghis Khan’s territory was uninhabited grassland. As a result, the size of his territory becomes almost meaningless. What use is holding a territory if there is nobody in it to exercise power over? The areas he controlled were mostly occupied by other nomadic tribes, which he simply gained control over. Very few cities and large settlements, and very little infrastructure were seized by Khan's armies.
Additionally, he did not dictate a clear ideological or cultural doctrine to the lands he possessed. While some Mongol practices were adopted and implemented, local cultures largely went unchanged under Mongol administration. They were simply unified by an individual, but nothing deeper.