To cope with the increasing complexity and constantly changing capability requirements of system-of-systems, an architectural approach for capability mapping and gap analysis is proposed. Firstly, a more specific architecture framework is presented. Secondly, on the basis of the analysis of the semantic relationships between constituent architecture data elements, a capability mapping approach is proposed to manage the relations between capabilities and systems based on the mapping matrixes representing associations of core entities. Then, a four-step capability mapping process for the mapping from capabilities to systems is suggested. Moreover, the capability gap analysis on how to identify and fill the capability gaps is also studied. Finally, an example of specific Net-Centric Warfare mission of Precision Engagement is used to illustrate the feasibility of the approach.