The study of natural vegetation of geological and historical periods in the Loess Plateau is an important scientific and practical issue for the development of northwestern China. However, interpretation of the natural vegetation before human reclamation is still controversial. The paper aims to analyze the potential factors that cause the difference in knowledge of Holocene natural vegetation developing in different topographies of the Loess Plateau. The distribution of paleovegetation in this region shows significant difference among rocky mountains, valleys, and Yuan lands (the plain area), i.e. it does not follow the natural vegetation zonation, as that in eastern China does. The Yuan lands with thick loess accumulation were never covered by a vast of dense forests during the Holocene. Forests (or open forests) developed preferably in valleys in the southern part of the Plateau and rocky mountains on the Plateau during the warm period of the Holocene. Some of local vegetation outside of the Loess Plateau are more subjected to the control of geomorphology and ground water.