Summary: Development of efficient model-updating and parameter estimation techniques is of great importance for civil structures. The present paper extends a recently developed cross-model cross-mode (CMCM) method for model updating and parameter estimation, when connectivity flexibility and boundary conditions are incorporated. First, the stiffness matrix of a beam member with semi-rigid joints at both ends is formulated, where the semi-rigid joints enable connections to be modelled as partially restrained. Second, boundary substructure elements are used to capture the stiffness and mass properties of the foundation. Finally, the model updating and parameter estimation of connection flexibility and boundary conditions are incorporated into the CMCM method. To validate the capability and effectiveness of the developed algorithm, numerical studies are conducted on a 2D bridge structure based on data generated from finite-element models. Numerical results demonstrate that the present method is effective for model updating and parameter estimation, when incorporating connectivity flexibility and boundary conditions.