Underground coal mining inevitably causes ground fissures, especially permanent cracks that cannot be closed at the boundary of the working face. Studying the underground three-dimensional morphology of the permanent cracks allows one to accurately constrain the formation and development of the ground fissures. This information will contribute to reducing mine disasters and is also a prerequisites to avoid environmental pollution. We selected the Zhangjiamao coal mine (China), which is situated in a collapsible loess area, as a case study for deciphering the formation of permanent cracks. After injecting gypsum slurry into the mine, a three-dimensional model of the ground fissures is obtained by three-dimensional (3D) laser scanner technology that records the 3D underground morphology. Integrating the geological context of a collapsible loess area, the characteristics and main processes of the ground fissure development are constrained: (1) The width of the ground fissure decreases to 0 with increasing depth and is strongly affected by the soil composition. (2) Along the vertical extension direction, the ground fissures are generally inclined to the inner-side of the working face, but the direction remains uncertain at different depths. (3) The transverse propagation direction of the ground fissure becomes more complex with increasing depth. (4) Under the influence of soil texture and water, loose soil fills the bottom of the ground fissure, thus affecting the underground 3D morphology.