The growth and decay of plant root systems can have destructive effects on earthen heritage sites, challenging permanent conservation of those precious sites. In this study, ground penetrating radar was used to detect the root systems of Populus gansuensis in ruins of the Ming Dynasty Great Wall of Gaotai, Gansu province. The results showed that the plan root systems of P. gansuensis distributed mainly in the north side of the ruins, extending from south to north. The lateral roots distributed around the plant taproot. The plant root systems of P. gansuensis distributed mainly at a the depth of 35~85 cm. The diameter of the taproot is about 12cm. The maximum measurable depth that the 400MHz antenna could reach was 200 cm below the surface. However, the detection precision of a 900MHz antenna is much greater than that of a 400 MHz antenna. If both were used, more information could be obtained on the growth status and the range of distribution of plant rood systems. For the first time, three-dimensional images of the root system were provided by the portable ground penetrating radar technology. Furthermore, the depth and location of the underground root system can be confirmed in a nondestructive way. This technology provides important scientific information for the protection and consolidation of the Great Wall site.