Civil engineering structures usually consist of a large number of members connected by joints. The joints are fixed with different types of fasteners, and they provide a certain amount of flexibility towards the static and dynamic behavior of the structure. Model updating of such a structure in practice is to improve the substructures followed by the joint property identification. This paper presents a method to update a super-element model of such a structure. The parameter selection strategy of generic element is adopted and the joint stiffnesses are treated as generic parameters to be updated simultaneously together with other structural parameters. An experiment with a three-dimensional steel truss is studied to illustrate the efficiency of the proposed method.