In this paper we propose a "Discrete Duality Finite Volume" method (DDFV for short) for the diffuse interface modelling of incompressible flows. This numerical method is, conservative, robust and is able to handle general geometries and meshes. The model we study couples the Cahn-Hilliard equation and the unsteady Stokes equation and is endowed with particular nonlinear boundary conditions called dynamic boundary conditions. To implement the scheme for this model we have to define new discrete consistent DDFV operators that allows an energy stable coupling between both discrete equations. We are thus able to obtain the existence of a family of solutions satisfying a suitable energy inequality, even in the case where a first order time-splitting method between the two subsystems is used. We illustrate various properties of such a model with some numerical results.