An approach of 3D craniofacial geometry shape similarity estimation is proposed to solve the problem that current approaches mainly rely on subjective assessment for the lack of related quantities. In our approach the cranioface

which is to be compared

is transformed into another one in the database and its principal warps are computed to be the base for the representation of the shape change. First

the global landmarks are selected from the two craniofaces and the thin-plate spline function is used to establish a map between them. Then

the corresponding bending transformation matrix is computed. This matrix can be represented by the product of the principal warps and one coefficient matrix

which is used to measure the deformation degree of the craniofaces. Finally

the geometry similarity distance is defined on the basis of the coefficient matrix. Experimental results demonstrate the feasibility and effectiveness of the approach.