Phononic crystals (PCs) are a novel class of artificial periodic structure, and their band gap (BG) attributes provide a new technical approach for vibration reduction in piping systems. In this paper, the vibration suppression performance and natural properties of fluid-conveying pipes with periodically varying cross-section are investigated. The flexural wave equation of substructure pipes is established based on the classical beam model and traveling wave property. The spectral element method (SEM) is developed for semi-analytical solutions, the accuracy of which is confirmed by comparison with the available literature and the widely used transfer matrix method (TMM). The BG distribution and frequency response of the periodic pipe are attained, and the natural frequencies and mode shapes are also obtained. The effects of some critical parameters are discussed. It is revealed that the BG of the present pipe system is fundamentally induced by the geometrical difference of the substructure cross-section, and it is also related to the substructure length and fluid–structure interaction (FSI). The number of cells does not contribute to the BG region, while it has significant effects on the amplitude attenuation, higher order natural frequencies and mode shapes. The impact of FSI is more evident for the pipes with smaller numbers of cells. Moreover, compared with the conventional TMM, the present SEM is demonstrated more effective for comprehensive analysis of BG characteristics and free vibration of PC dynamical structures.