The formula to calculate the natural frequencies of a moving mass and beam coupled system was established. First, in the case of a moving mass made decelerated motion, the fundamental frequency of the coupled system can be gained by getting the deflection response curve of beam through the numerical simulation experimental method. Second, in the case of the moving mass made uniform motion, the fundamental frequency of the beam can be gained by getting the midspan deflection response curve of the beam through the numerical simulation experimental method. Third, the eigenvalue computation method can be used to get the various steps natural frequencies of the coupled system. The results of numerical examples show that the natural frequencies of the coupled system, not only have relation to the mass ratio, but also to the location ratio. Sometimes there will be bigger error if the natural frequencies of beam are used instead of the natural frequencies in coupled system or the theoretical values are substituted by the experimental values.