To investigate the identification of special-shaped water-rich micro-cracks in tunnel lining structures, ground-penetrating radar (GPR) was used to detect the water-filling models of four special-shaped micro-cracks. The F-K migration method was applied to offset and locate the radar characteristic signals of micro-cracks, with crack locations identified through waveform analysis and the wavelet modulus maximum algorithm. The results indicate that the radar response images of irregular micro-cracks are difficult to identify directly, while their morphology can be highlighted by the F-K migration method. Compared to waveform analysis, the wavelet modulus maximum algorithm provides more accurate positioning and identification of irregular micro-cracks. The two-dimensional contour reconstruction of the micro-fracture models fits the shape of the solid models. The research results provide a foundational basis for the identifying abnormal water-rich micro-cracks in tunnel lining structures.