The invention discloses a multi-reference time-domain transmissibility-based output-only structure modal parameter identification method and belongs to the structure dynamics technical field. According to the method of the present invention, collected response signals of an engineering structure are divided into a non-reference output signal group and a reference output signal group, wherein the non-reference output signal group and the reference output signal group are respectively adopted as the input and output of a multi-reference time-domain transmissibility model, and therefore, the modal identification problem of the structure under a non-white input condition can be processed, and the structure is not limited by load forms; a traditional transmissibility function defined in the frequency domain is expanded to the time domain, so that the conversion of time-domain data of the measurement output of the structure to the frequency domain can be avoided; and the time-domain data aredirectly adopted to perform modal analysis on the engineering structure, and therefore, so that the selection of window functions in the conversion process can be avoided, errors and adverse influence such as leakage and frequency resolution reduction during the conversion can be eliminated, the precision of modal parameter identification is improved, and requirements for the professional knowledge of a user can be lowered. The modal parameters of the structure which are recognized by the present invention can be applied to the engineering structure mechanics filed to solve practical engineering problems.