A pipe structure model composed of straight pipe, bent pipe, concentrated mass and flexible support was established. The axial, lateral and circumferential vibration of this model were taken into account in the paper. Then it was realized to calculate the natural characteristic of this pipeline in computer by using MATLAB language to program a series of procedures based on frequency-domain transfer matrix method. The calculation results were compared with the ANSYS simulation results, which illustrated the upper accuracy of frequency-domain transfer matrix method in calculating natural characteristic problems of pipeline structure system. At last, The pipeline system was analyzed with experimental modal method．By comparing the experimental results and computational results, relatively lesser error showed that computational results were reliable and frequency-domain TMM was verified to be valuable for practical application.