We show how the smooth geometry of Calabi-Yau manifolds emerges from the thermodynamic limit of the statistical mechanical model of crystal melting defined in our previous paper arXiv:0811.2801. In particular, the thermodynamic partition function of molten crystals is shown to be equal to the classical limit of the partition function of the topological string theory by relating the Ronkin function of the characteristic polynomial of the crystal melting model to the holomorphic 3-form on the corresponding Calabi-Yau manifold. This result suggests that the wall-crossing formula between the non-commutative and commutative Donaldson-Thomas theories becomes trivial in the thermodynamic limit.