Abstract: Effective heat conductivity and soil water flux are important in atmosphere-soil systems. Because of the lower cost and stability of the soil temperature instruments, the temperature tracer methods have been widely applied to estimating water flux. Yet, the non-ideal sine changes of soil temperature caused by clouds, precipitation and some other factors hinder the use of that method under the condition of forced sine changes of soil temperature. To overcome this default, the authors use the Dynamic Harmonic Regression method to extract the amplitude and phase of soil temperature and then apply the results to the analytical solution of incorporation of heat and water equation to calculate the effective thermal conductivity and water flux. The method was applied to the field experimental data collected from the Mau Us Desert. The analytical results show that: ①effective thermal conductivity changes are around 10-7m2/s and increase along with the increase of amplitude ratio and decrease of difference of phase; ②effective thermal conductivity increases liberally with soil water content when soil water content is smaller than 0.08, but remains at a certain value when soil water content is large than 0.08; ③there exists no obvious relationship between soil water flux and soil water content. The research results have the scientific and practical value for guiding the calculation of soil water flux.