Motivated by recent mathematical developements in non-commutative Donaldson-Thomas theory, we construct a new statistical mechanical model of crystal melting to count BPS branes wrapping an arbitrary toric Calabi-Yau 3-fold. We also discuss the wall crossing phenomena, which are crucial for the proper understanding of the relation between the crystal melting and the topological string theory. (Joint work with H. Ooguri, arXiv:0811.2801 and arXiv:0902.3996.)