Nowadays with great improvement in digital computation techniques and increasing numerical methods such as finite element method, still having an accurate analytical model of complex systems such as bolted joint in mechanical structures depends on results of experimental tests. One of the applicable experimental analysis methods is modal test, that can derivate structural dynamics parameters of a mechanical system such as natural frequency, mode shapes and modal dampings. In this paper the procedure of finite element model updating of a bolted joint of an aircraft wing and fuselage joint place is done. For this purpose, at first, an analytical model of problem is created and analyzed in a finite element software and then an experimental model is created and modal test is done. For comparing two models, an analytical model is reduced and then with converging these models an exact model of structure is produced. Finite element model updated with direct methods. Also the effects of some basic parameters of structure in finite element model data is investigated.