Inaccurate mass estimates have been recognized as an important source of uncertainty in structural identification, especially for large-scale structures with old ages. Over the past decades, some identification algorithms for structural states and unknown parameters, including unknown mass, have been proposed by researchers. However, most of these identification algorithms are based on the simplified mechanical model of chain-like structures. For a chain-like structure, the mass matrix and its inverse matrix are diagonal matrices, which simplify the difficulty of identifying the structure with unknown mass. However, a structure with a non-diagonal mass matrix is not of such a simple characteristic. In this paper, an online joint state-parameter identification algorithm based on an Unscented Kalman filter (UKF) is proposed for a structure with a non-diagonal mass matrix under unknown mass using only partial acceleration measurements. The effectiveness of the proposed algorithm is verified by numerical examples of a beam excited by wide-band white noise excitation and a two-story one-span plane frame structure excited by filtered white noise excitation generated according to the Kanai–Tajimi power spectrum. The identification results show that the proposed algorithm can effectively identify the structural state, unknown stiffness, damping and mass parameters of the structures.