In order to improve the accuracy of Portable Falling Weight Deflectometer (PFWD) in measuring the resilient modulus of high liquid limit soil subgrade, the influence of deformation lags effect on the back-calculation result was considered and a new method for back-calculation of 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 increase of subgrade modulus, the lag effect of the deformation is not significant. The back-calculating results via conventional and new methods are similar, but the accuracy of the new method is higher.