In order to improve the accuracy of Portable Falling Weight Deflectometer (PFWD) in determining the resilient modulus of high liquid limit soil subgrade, and considering the influence of deformation lags effect on the back-calculation result. A new method for back-calculating the modulus was proposed based on Kelvin viscoelastic model and quasi-static dynamic analysis method. The effectiveness of the new method is verified by field tests. The results show that the measured modulus of the lower embankment filled with high liquid limit soil is lower and the peak vertical displacement of the top surface of the embankment obviously lags behind the peak value of the load under the impact load of PFWD. Furthermore, the load-displacement curve is significantly nonlinear. In addition, the conventional method based on linear elastic model makes the back-calculated modulus much larger than the measured modulus. The average relative error between back-calculated and the measured modulus reaches up to 52.5%. However, the new method can better reflect the deformation lag characteristics under impact load. The average relative error between them is only 9.2%. With the increase of subgrade modulus, the lag effect of the deformation is not significant. The back-calculating results of conventional and new methods are similar, but the former is still much larger than the latter. The modulus back-calculated by the new method can be used as the basis for construction quality control of high liquid limit soil subgrade.