The hidden structural disease of the airport runway pavement seriously threatens the safety of the operational aircraft. In order to accurately and timely detect the bearing capacity of the pavement structure and accurately identify the internal structural diseases, the non-destructive testing technology research is carried out based on the runway surface of Guangdong Baiyun Airport. Inversion of the elastic modulus of the pavement structure by the deflection cone method obtained by the drop hammer deflection method, combined with the coefficient of transfer ratio between the cement plates, can comprehensively evaluate the pavement cement with low bearing capacity and low modulus. In the board, the deflection between the plates is smaller than the transfer coefficient, and there is a good mapping relationship between the two. The three-dimensional ground penetrating radar technology is used to detect the internal disease of the pavement structure layer. It is found that the deflection and deformation of the force-transmitting rod occur in the position where the deflection is lower than the transfer coefficient, and the interior of the concrete slab is broken and the water is accumulated at the joint. It is recommended to carry out different treatment measures according to diseases. The combination of two non-destructive testing technologies can efficiently detect and evaluate the road surface performance of the runway, and provide an accurate and reliable technical basis for the detection and treatment of pavement diseases.