We propose a generalization of the topological vertex, which we call the "non-commutative topological vertex". This gives open BPS invariants for a toric Calabi-Yau manifold without compact 4-cycles, where we have D0/D2/D6-branes wrapping holomorphic 0/2/6-cycles, as well as D2-branes wrapping disks whose boundaries are on D4-branes wrapping non-compact Lagrangian 3-cycles. The vertex is defined combinatorially using the crystal melting model proposed recently, and depends on the value of closed string moduli at infinity. The vertex in one special chamber gives the same answer as that computed by the ordinary topological vertex. We prove an identify expressing the non-commutative topological vertex of a toric Calabi-Yau manifold X as a specialization of the closed BPS partition function of an orbifold of X, thus giving a closed expression for our vertex. We also clarify the action of the Weyl group of an affine A L Lie algebra on chambers, and comment on the generalization of our results to the case of refined BPS invariants.Recently, there has been significant progress in the counting problem of BPS states in type IIA string theory on a toric Calabi-Yau 3-fold 1 . In the literature, the Calabi-Yau manifold (which we denote by X) is assumed to have no compact 4-cycles, and we consider a BPS configuration of D0/D2-branes wrapping compact holomorphic 0/2-cycles, as well as a single D6-brane filling the entire Calabi-Yau manifold. The question is to count the degeneracy of such BPS bound states of D-branes.One subtlety in this counting problem is the wall crossing phenomena, stating that the degeneracy of BPS bound states depends on the value of moduli at infinity. Indeed, the closedwhich is defined in [3] as the generation function of the degeneracy of D-brane BPS bound states 3 , depends on maps σ ′ , θ ′ specifying a chamber in the Kähler moduli space 4 . What isinteresting is that in one special chamberC top of the Kähler moduli space, the BPS partition function is equivalent the topological string partition function 5 (up to the change of variables, which we do not explicitly show here for simplicity): , 2, 3, 4, 5, 6, 7]. See also [8,9,10,11,12,13,14] for mathematical discussions 2 The upper index c stands for 'closed'. 3 The definition of the partition function Z BPS is the same as the partition function Z BH in [15]. 4 See Appendix A for details. 5 Actually, the topological string partition function depends on the choice of the resolution of the singular Calabi-Yau manifold X. This is related to the choice of the limit, as will be explained in the main text. 6 The upper index o stands for 'open'. 7 The word 'non-commutative' stems from the mathematical terminologies such as "non-commutative crepant resolution" [19] and "non-commutative Donaldson-Thomas invariant" [8]. The non-commutativity here refers to that of the path algebra of the quiver. The quiver (together with a superpotential) determines a quiver quantum mechanics, which is the low-energy effective theory on the D-brane worldvolume [3]. 9 See [6] f...