In order to describe the degree of the structure damage which caused by the crack in the rectangular beam, a method for measuring the crack flexibility based on the natural frequencies is presented. Firstly, the first three order natural frequencies of the rectangular beam were resolved by dynamics analysis, the natural frequency database with various crack locations and flexibilities was set up, and then the surface-fitting technique was employed to draw the natural frequency influence surfaces. Secondly, the vibration signal of the rectangular beam was tested, and the first three order natural frequencies could be obtained. Thirdly, these frequencies measured were adopted to cut the natural frequency influence surfaces, and then the first three order natural frequency influence curves were drawn. The intersection points of these frequency influence curves could indicate the crack flexibility and the corresponding crack location. The results showed that the presented method could effectively measure the crack flexibility and the corresponding crack location. Furthermore, it could be seen from the measurement process of the crack flexibility that the input parameters for drawing the natural frequency influence surface were a series of sample points of the crack locations and flexibilities. These input parameters had no relation to the type of crack, the shape of crack and the calculation formula of the crack flexibility. It can be concluded that the presented method can be used to measure the flexibility of the crack with different type and shape in the rectangular beam and can provide an important reference for the study of the dynamics analysis and damage identification of the beam with crack.