The invention discloses a layered measurement method of similarities of a complex surface-shaped entity scene with holes. The complex surface-shaped entity scene with the holes is divided into a complex scene layer, a micro-scene layer and a simple entity layer; the relation of the adjacent layers is regarded as a set relation, the similarities of all the layers are mutually embedded, entity matching is conducted from top to bottom, similarity calculation is conducted from being locally to being globally, and then a similarity measurement result of the complex surface-shaped entity scene withthe holes is obtained. The layered measurement method is applicable to studying the more complex surface-shaped entity scene with the holes.