A methodology is developed for eliminating the transducer mass loading effects (TMLE) from time-domain response in this paper. By utilizing the measured free vibration response, the modal parameters including the effects of transducer mass loading are firstly identified by the eigensystem realization algorithm. Then, the initial finite element model of the target structure with the transducer mass loading effects is updated with the experimental modal parameters, and the changes of modal parameters with and without transducer mass are predicted with the updated finite element model by removing the transducer mass. After that, a set of identification equations for eliminating the TMLE are set up based on the modal superposition method, and the TMLE are eliminated from the original measured time-domain response with the previously predicted changes of modal parameters. Finally, the proposed methodology is verified through the dynamic test carried out for a laboratory beam with clamped-clamped boundary conditions.