The dynamic characteristic parameters of Up-time of Flight Counter (U-ToFC) are important for research of structure optimization and reliability. However, the current simulation is performed based on homogenous material and simplified constraint model, the correct and reliability of results are difficult to be guaranteed. The finite element method based on identification of material parameters is proposed for this investigation on dynamic analysis, simulation and vibration experiment of the U-ToFC. The structure of the U-ToFC is complicated. Its’ outside is made of aluminum alloy and inside contains electronic components such as capacitors, resistors, inductors, and integrated circuits. The accurate material parameters of model are identified difficultly. Hence, the parameters identification tests are performed to obtain the material parameters of this structure. On the basis of the above parameters, the experiment and FEA are conducted to the U-ToFC. In terms of the flight acceptance test level, and two kinds of joints condition between the U-ToFC and fixture are considered. The natural frequencies, vibration shapes and the response of the power spectral density of the U-ToFC are obtained. The results show simulation which is based on parameters identification is similar with vibration experiment in natural frequencies and responses. The errors are less than 10% . The vibration modes of simulation and experiment are consistent. The paper provides a more reliable computing method for the dynamic characteristic analysis of large complicated structure. The dynamic characteristic parameters of Up-time of Flight Counter (U-ToFC) are important for research of structure optimization and reliability. However, the current simulation is performed based on homogenous material and simplified constraint model, the correct and reliability of results are difficult The finite element method based on identification of material parameters is proposed for this investigation on dynamic analysis, simulation and vibration experiment of the U-ToFC. The structure of the U-ToFC is complicated. Its’ outside is made of aluminum alloy and inside contains electronic components such as capacitors, resistors, inductors, and integrated circuits. The accurate material parameters of models are and was confirmed difficultly. above parameters, the experiment and FEA are conducted to the U-ToFC The natural frequencies, vibration shapes and the response of the power spectral density of the U-ToFC are obtained. The results show simulation which is based on parameters The errors are less than 10%. The vibration modes of simulation and experiment are consistent. The paper provides a more reliable computing method for the dynamic characteristic analysis of large complicated structure.