For the applications of TDR system in measuring water content, FDTD equations were obtained based on the propagation equations of electromagnetic wave. Using the equations the program was compiled in Matlab for simulation. Through comparing simulating curve and test curve it turns out that the simulating curve accords with test curve well for water content measuring TDR system in homogeneous medium, whereas the simulating curve does not for analog coaxial cable system in layered medium, although the inflexi...