The samples to be measured with infrared instrument are usually required to be homogeneous. However, discontinuous sample is quite common in the real infrared measurements, such as, high viscosity liquids containing air bubbles. In this paper, the spectral distortion of discontinuous sample was analyzed with simple theoretical simulation and experimental examples quantitatively. The spectral properties of the discontinuous sample were studied and discussed systematically. Both theoretical computation and experimental results demonstrated that the infrared spectrum of a discontinuous sample was highly similar to that of the uniform sample if suitable experimental conditions were adopted. Our results showed that if infrared samples can be prepared to be thin enough, the infrared spectrum of the discontinuous sample can fulfill the requirements of analysis work nearly perfectly.