The frequency spectrum generated by the Fast Fourier Transform (FFT) of the vibration waveform data is one of the commonly used plots for vibration analysis and fault diagnosis. It is a common diagnosis method using the harmonic components in the spectrum to analyze the cause of abnormal vibration of compressor unit. However, due to the complex causes of harmonic components, the accuracy of vibration analysis may easily be adversely affected. Therefore, this paper studies the causes of harmonic generation. By means of simulation calculation and casestudy verification, it is proven that the significant superposition of complex frequency components in the vibration waveform or the existence of periodic mutation in the waveform will lead to the emergence of harmonics in the spectrum. Analyzing the root causes of harmonic generation will help to identify the causes of fault, evaluate the fault severity, formulate maintenance plan, and provide robust guarantee for the safe operation of centrifugal compressor unit in the long-distance natural gas transmission pipeline.