In order to obtain the particle temperature in complex plasmas, a new method based on the pair distribution function (PDF) is investigated. From the PDF, the mean square displacement is obtained. To estimate the temperature, the particle motion is also traced. The fast Fourier transform (FFT) analysis of the motion data indicates that the fundamental and second harmonic frequencies are found. The model for a single frequency is expanded to calculate the temperature under the multiple frequencies conditions. The temperature is estimated to be 0.08 to 0.17 eV. This is consistent with the temperature obtained from the conventional method.