Stress waves propagate along vertical, radial and circumferential directions when a non-uniformly distributed load is applied at one end of a three-dimensional shaft. As a result, the receiving signals are usually mixed with undesired interference components, often featuring as high-frequency fluctuations. Previous studies have revealed that sectional geometry (shape and size) greatly affects the high-frequency interference. In this study, low strain dynamic testing on full-scale X-section concrete is conducted in order to investigate the influences of high-frequency interference on velocity responses at the pile head. Emphasis is placed on the frequency and peak value of interference waves at various receiving points. Additionally, the effects of the geometrical, and mechanical properties of the pile shaft on high-frequency interference are elaborated on through the three-dimensional finite element method. The results show that the measured wave is obscured by interference waves superposed by two types of high-frequency components. The modulus and cross-sectional area are contributing factors to the frequency and peak value of the interference waves. On the other hand, the position with the least interference is determined, to some extent, by the accurate shape of the X-section.