Abstract: Identification of mechanical connections plays a significant role in predicting the dynamic behavior of an assembled structure. Due to the noise affection and the difficulty to directly use the measurable data to identify the dynamic properties of the joint with traditional methods based on substructure decoupling, a new method is proposed. Firstly, the components of the basic equation of substructure decoupling on the measurement degree of freedoms (DOFs) are extracted, and the form containing the joint dynamic stiffness matrix is obtained by matrix transformation. Then, the real joint dynamic stiffness matrix is decomposed into a known initial matrix and an incremental matrix to be solved, and the incremental iterative equation with convergence property is derived to enhance the numerical stability of identification when the number of interface DOFs is extremely large. Polynomial fitted dynamic stiffness is used to form a frequency domain estimation equation of fitting coefficients representing joint properties. By selecting appropriate frequency points to simultaneous equations according to the given criteria, an iterative formula for identifying joint properties is obtained, in which only the measurement frequency response functions (FRFs) of the assembly are needed. Finally, a numerical example and an experimental example are provided to verify the method and to describe the identification procedure. Numerical simulation of a 10-DOFs spring-mass system verifies the correctness and anti-noise of the proposed method. Tests and identifications are also carried out on a T-shaped beam structure with one adhesive connection and a L-shaped beam structure with two bolted connections. The result shows that the FRFs calculated by the finite element model (FEM) of the assembly recombination by the residual structure and the identified joint is in good agreement with the measured values in a wide frequency band, which indicates the effectiveness of this method in identifying the joint properties in the actual assembly structure.