Abstract The karst cavern is common undesirable geological body in limestone areas, which can bring great safety hazards to the construction and operation of tunnels, bridges and highways. Transient electromagnetic method (TEM) can effectively detect hidden karst structures based on the difference in electrical property between the karst cavern and the surroundings. Traditionally, 1D inversion is commonly used for the interpretation of TEM data due to its high efficiency. However, this may lead to artifacts due to 2D or 3D effects in practical surveys. In this study, we present a Gaussian-Newton approach to 3D inversion of TEM data for karst cavern detection. The numerical test on synthetic TEM data demonstrates that 3D inversion can effectively delineate the location and geometry of concealed karst cavern compared to the 1D inversion results.