With the advancement of reconfigurable tooling and manufacturing systems, aerospace enterprises are looking for mixed production solutions to gain leading competitive edge. An accurate similarity metric will be necessary and crucial for making sound mix-production decisions. Most literatures studied similarity coefficients for grouping part families in cellular manufacturing systems; however they are not applicable to aircraft assemblies which involve large amount of manual work dealing with large heavy components and assemblies. This paper proposes a new similarity metric that incorporates both component level similarity and system level similarity of aircraft assemblies. The similarity in components level is modeled based on part-operation and operation-operation incidence matrices. The similarity in assembly level is modeled by similarity system theory associated with a newly proposed operation quota based weighting method. A digital manufacturing tool has been developed for the automated implementation of the new models. Both the models and the tool have been validated by six pairs of real life panel-assembly examples. Results showed that the new similarity index gives clear indication to the degree of commonality in panel assemblies, and the digital tool can generate the similarity results rapidly and accurately.