Application of geophysical methods has increased to investigate near-surface horizons of interests in related to environmental and engineering geophysics because geophysical methods are cost-effective and large areas can be quickly surveyed at relatively low cost without borings and trench excavations. The most productive geophysical methods are Ground Penetrating Radar and Electrical Resistivity methods for which the target exhibits the greatest physical contrast with respect to the surrounding formations. However, the geoelectrical geophysics is very difficult to predict the sub-surface using conventional techniques because of the shortage of the resolution. These geophysical techniques have required upgrading of data acquisition accuracy of the methods using a multichannel resistivity tool such as Handy Archaeological Resistivity Meter developed by the joint research of Kyushu University and OYO Corporation in Japan. Geoelectrical methods have the economic advantages to solve various archaeological problems. However, there was no successful 3D computer program required for interpreting observed apparent resistivity data. In the present paper, a robust 3D computer program was developed and applied to archaeological prospection. Results of 3D inversion of VES data are compared with the results of GPR method and evaluated with archaeologists of Archaeological Society of Japan.