Jointed structures are widely used in engineering applications, and local nonlinear characteristics at the connection interface have an important influence on their dynamic modeling and characteristic prediction. Aiming at the problem that local connection parameters of nonlinear structural systems are unknown or difficult to measure, this paper proposes an identification method of local linear connection stiffness based on the FRF transformation from the perspective of inverse dynamic problems. By further combining with the time-domain nonlinear subspace identification method, the local linear and nonlinear connection stiffness of nonlinear structural systems can be finally obtained. The numerical example and experimental setup of the three degrees-of-freedom structural system are designed and further built to validate the proposed method. The results demonstrate that the proposed method can separate and identify the underlying linear FRF and nonlinear parameters of the nonlinear structural system, and subsequentlly realize the joint identification of the local linear and nonlinear connection stiffness.