Abstract: According to the first and second principles of thermodynamics, the influence of the magnitude of radio-frequency voltage and variations of duty ratio on the heat of high-field asymmetric waveform ion mobility spectrometry (FAIMS) is studied. The absolute value of heat produced by migration tube of FAIMS increases with increasing size of radio-frequency voltage. However, the absolute value is smaller with increasing duty ratio. The result shows that a change in radio-frequency voltage could lead to the temperature difference generated by FAIMS system,which causes the heat transfer and then affects the reliability and stability of FAIMS. By theoretical analysis and algorithm processing, it can be found that the influence of the temperature caused by the performance of the system on FAIMS is minimal when duty ratio is 0.1 and radio-frequency voltage is 2 700 V, which provides essential data for the design of portable FAIMS.