SummaryFlexibility is an important parameter reflecting bridge load‐carrying capacity. Dynamic testing is a fast and effective method to obtain the structural modal flexibility of small‐ and medium‐span bridges. The Deterministic‐stochastic subspace identification (DSI) algorithm is a well‐established structure identification method in the time domain. However, the estimation of damping, especially the modal scaling factor, is not always reliable due to inevitable measurement noise, which directly affects the identification accuracy of flexibility. This paper proposes a maximum likelihood estimation method in subbands (SMLE), which can be regarded as an add‐on method of the DSI algorithm because the initial parameters are obtained from the DSI algorithm. The processing of frequency band division is implemented first, and the frequency response function curve in each subband of the whole frequency range is fit separately. Then, subband cyclic iteration is proposed to improve the identification accuracy in a closely spaced mode system. The proposed SMLE method maintains the advantages of the DSI algorithm while improving the accuracy of parameter estimation and flexibility identification. Two lumped mass models are used to verify that the proposed method can effectively improve estimates to obtain a precise flexibility matrix and predict the displacement of the structure under static loading. Experimental example of a continuous girder bridge is considered to verify the availability and effectiveness of the proposed method in practice.