This paper proposed a time domain measurement method of characteristic impedance based on TDR, because frequency domain measurement of the characteristic impedance is difficult to meet the needs of industrial production. This paper measured characteristic impedance of the standard circuit board using the TDR module Agilent54754A, and imported the text data of the experimental measurement from the oscilloscope to the computer as the measured data of circuit board characteristic impedance calculation. However, the measured data from the time domain measurement method is susceptible to time base jitter and the microwave reflection, the paper eliminated timebase jitter of data by PDF deconvolution method effectively, and removed the microwave reflection by selecting the best measurement zone in accordance with IPCTM650 regulations effectively, and integrated of two methods to process the experiment data. By transforming the voltage value into the impedance value, the results showed that data processing results are very close to the calibrated value of DUT.