We apply the relation between deep learning (DL) and the AdS/CFT correspondence to a holographic model of QCD. Using a lattice QCD data of the chiral condensate at a finite temperature as our training data, the deep learning procedure holographically determines an emergent bulk metric as neural network weights. The emergent bulk metric is found to have both a black hole horizon and a finite-height IR wall, so shares both the confining and deconfining phases, signaling the cross-over thermal phase transition of QCD. In fact, a quark antiquark potential holographically calculated by the emergent bulk metric turns out to possess both the linear confining part and the Debye screening part, as is often observed in lattice QCD. From this we argue the discrepancy between the chiral symmetry breaking and the quark confinement in the holographic QCD. The DL method is shown to provide a novel data-driven holographic modeling of QCD, and sheds light on the mechanism of emergence of the bulk geometries in the AdS/CFT correspondence.