In this paper, we discuss a relation between Jones-Witten theory of knot invariants and topological open string theory on the basis of the volume conjecture. We find a similar Hamiltonian structure for both theories, and interpret the AJ conjecture as the D-module structure for a D-brane partition function. In order to verify our claim, we compute the free energy for the annulus contributions in the topological string using the Chern-Simons matrix model, and find that it coincides with the Reidemeister torsion in the case of the figure-eight knot complement and the SnapPea census manifold m009.The hyperbolic three-manifold M is given bywhere Γ is a torsion-free and discrete subgroup of P SL(2; C) with the action (2.2).The volume of an ideal tetrahedron T αβγ is computed directly by using the metric (2.1) [33].The function Λ(θ) is called the Lobachevsky function. The volume formula can also be rewritten in terms of the Bloch-Wigner function D(z)(2.9)The gluing condition along each edge imposes constraints on the face angles of the ideal tetrahedra.(2.10)Furthermore, we should also consider the gluing condition for the boundary of the knot complement. In order to realize the torus as a boundary, the face angles must satisfy the completeness conditions along the meridian and the longitude.Mostow's rigidity theorem [34] implies that these conditions are solved uniquely with Im z i > 0 for all i. By summing all volumes for the ideal tetrahedra, we are able to determine the hyperbolic volume uniquely for each hyperbolic three-manifold.