The invention discloses a method for identifying the inertial parameters of a six-degree-of-freedom parallel mechanism, which comprises the following steps of: performing sine excitation with the same frequency respectively in six degree-of-freedom directions, decomposing the pose and the exciting force signal into the Fourier series form by using the least square fit principle, extracting the sine and cosine signal components of the fundamental frequency, and solving a specific linear equation set to obtain the inertial parameter matrix of the parallel mechanism. The method has the advantages of high identification accuracy, simple operation, high automation degree in identification process and small interference by system nonlinear factors (Coriolis force, Coulomb friction force and the like).