The invention relates to an invisible disease detection method of a pavement structure layer, which comprises the steps of detecting a pavement with a road ground penetrating radar and an excitation pavement acoustic generator, obtaining a modulus of resilience of the pavement structure layer according to detected data, analyzing a strength characteristic of the pavement structure layer of a detected road section according to the modulus of resilience, and exactly detecting positions and sizes of invisible diseases such as cavities and looseness in the pavement. The method can quickly, accurately and continuously detect the invisible diseases such as the looseness, the cavities, interlayer discontinuity and poor strength in the structure layer of the pavement of forms such as highways of various grades, urban roads and airfield runways, provides complete data for evaluating the detected pavement, provides bases for implementing road prevention and maintenance, provides data support for maintenance decisions within the service life of the road, reduces interference with traffic, is nondestructive, reduces secondary damages to the pavement, saves cost, reduces energy consumption, increases social benefits, and can evaluate structural conditions of the pavement more completely and reasonably.