Geometric morphometrics(GM)originated from late 1980s to early 1990s in last century.It differed from the traditional measurement,mainly focusing on the variability of shape.With relative theory foundation,we were separating shape from size,explaining the intrinsic results using multivariate analysis.This new method was meaningful to the organism with fixed and stable shape,and also widely used in many fields.Generally,aquatic animals were surrounded by hard structures with relatively invariable shape.Meanwhile,they played different important roles in diversified waters.This paper reviewed the shape analysis of aquatic animals with geometric morphometrics in the recent decades,briefly described the developing process of this new method,explained the principles of outline and landmark method,and introduced methodology and some relevant software.Then we retrospected the application of invertebrate and vertebrate morphological shape in aquatic area.The result showed that this new approach was accepted by many researchers at home and abroad,but had a limitation in species identification and population division,so we should use the hard structures to analyze the morphological variation,consider the implication of environmental change with the morphology of organism,and try to print out the original appearance in 3D and describe the shape variation with theoretical studies.