We consider a string dual of a partially topological $U(N)$ Chern-Simons-matter (PTCSM) theory recently introduced by Aganagic, Costello, McNamara and Vafa. In this theory, fundamental matter fields are coupled to the Chern-Simons theory in a way that depends only on a transverse holomorphic structure on a manifold; they are not fully dynamical, but the theory is also not fully topological. One description of this theory arises from topological strings on the deformed conifold $T\ast S3$ with $N$ Lagrangian 3-branes and additional coisotropic `flavor' 5-branes. Applying the idea of the Gopakumar-Vafa duality to this setup, we suggest that this has a dual description as a topological string on the resolved conifold $O(-1)\oplus O(-1)\to \mathrm{CP}1$, in the presence of coisotropic 5-branes. We test this duality by computing the annulus amplitude on the deformed conifold and the disc amplitude on the resolved conifold via equivariant localization, and we find an agreement between the two. We find a small discrepancy between the topological string results and the large $N$ limit of the partition function of the PTCSM theory arising from the deformed conifold, computed via field theory localization by a method proposed by Aganagic et al. We discuss possible origins of the mismatch.