Steel ingot with a large height-to-diameter ratio is utilized to produce multiple products by one stock in practice. Water cooling is a usual way to enhance production efficiency. However, the combination of the two factors will generate internal defects, such as shrinkage porosity and hot crack. The characteristic of internal shrinkage crack in a 10 t water-cooled steel ingot with a large height-to-diameter ratio was examined by an ultrasonic test. A slice was sectioned from the ingot middle part where billets containing star-like crack were further extracted. The billets were examined by X-ray high energy industrial CT, and the compactness was reconstructed in three dimensions. Microstructure near the crack was observed using scanning electron microscopy, and the solidification process and grain size were studied by high temperature confocal microscopy. Moreover, thermo-mechanical simulation and post-processing were carried out to analyze the formation of shrinkage porosity and hot crack. A new criterion considering mushy zone mechanical behavior in brittle temperature as well as grain size distribution was proposed to evaluate hot cracking potential in the ingot. The results show that a deep shrinkage porosity band easily forms in the center line of such an ingot with a large height-to-diameter ratio, and water-cooling further generates excessive tensile stress tearing the liquid films around the porosities. Then, hot cracks begin to propagate along grain boundaries. The grain size in the upper and center of the ingot is large, which leads to an inverted cone shape defects zone in the ingot center.