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System of Systems (SoS) capability has two forms - Capability Requirement (CR) and Capability Property (CP). This paper emphasizes on the emergence process of CP. A double layer CP modeling framework is proposed based on the complexity analyzing of SoS relationships, and the key modeling technique has discussed. The double layer framework addressed a modeling process from micro mechanism modeling to macro behavior distinguishing. The micro mechanism modeling is creating network model of SoS relationship based on analyzing and formalizing SoS complex relationship, and the macro behavior distinguishing is recognizing SoS CP based on aggregating capability index system. The framework researches in SoS internal complex relationship from the prospective of capability, focuses on relationships which have major influence on the CP, and induces the consequence of relationships through nonlinear process modeling.