In energy harvesting systems, specifications of the generated electrical energy depend on the structure’s dynamics. This dependence can be used to identify the system’s joint characteristics. To this end, an innovative frequency-response-function (FRF) based identification method is presented. The investigated system is a cantilever beam shaped structure with an embedded bimorph piezoelectric bender, connected to a base via bolted joint as a depiction for wing of a UAV connected to fuselage. The implemented FRF is ratio of the piezoelectric output voltage to the base input displacement. The joint identification procedure consists of analytical modeling of the system with joint, experimental testing of the system and a real-coded Genetic Algorithm (GA) method. The joint is modeled as a combination of longitudinal and torsional springs, whose stiffnesses are obtained using the GA method. The obtained results indicate that the analytical model has good correlation with the experimental data. Then, effects of the joint characteristics on the energy harvester’s performance are investigated by comparison of the system with two different joint assumptions, namely, rigid and realistic joint. Finally, the effects of various joint characteristics on the energy harvester’s performance are presented and approaches to achieve the maximum performance of the system are suggested.