We formulate large N duality of U(N ) refined Chern-Simons theory with a torus knot/link in S 3 . By studying refined BPS states in M-theory, we provide the explicit form of low-energy effective actions of Type IIA string theory with D4-branes on the Ω-background. This form enables us to relate refined Chern-Simons invariants of a torus knot/link in S 3 to refined BPS invariants in the resolved conifold. Assuming that the extra U(1) global symmetry acts on BPS states trivially, the duality predicts graded dimensions of cohomology groups of moduli spaces of M2-M5 bound states associated to a torus knot/link in the resolved conifold. Thus, this formulation can be also interpreted as a positivity conjecture of refined Chern-Simons invariants of torus knots/links. We also discuss about an extension to nontorus knots.Dedicated to John H. Schwarz on his 75th birthday 1 Charges of J1, J2 and SR are normalized to be half-integers. 2 The brane setting gives rise to U(N ) gauge group instead of SU(N ) gauge group. However, the U(1) part merely provides the correction due to the framing number as well as the linking number of a knot/link, which play no role in this paper. Therefore, the difference between U(N ) and SU(N ) invariants will be ignored in this paper. 3 We denote the unreduced invariants by rCS λ (Tm,n; a, q, t) and the reduced invariants by rCS λ (Tm,n; a, q, t)where they are related by rCS λ (Tm,n; a, q, t) = rCS λ ( ; a, q, t) rCS λ (Tm,n; a, q, t) .where the function g λ can be determined by using the unknot invariants and it turns out to be the Macdonald norm defined in Appendix A. At the unrefined limit q = t, it reduces to the generating function of SU(N ) quantum invariants J SU(N ),λ (T m,n ; q) first obtained in [OV00] Z def,SU(N ) = λ J SU(N ),λ (T m,n ; q) s λ (x) , where s λ (x) are the Schur functions.