A finite difference numerical scheme is proposed for the Cahn-Hilliard-Stokes system with Flory-Huggins energy functional. A convex splitting method is applied to the chemical potential, which in turns leads to the implicit treatment for the singular logarithmic terms and the surface diffusion term, and an explicit update for the expansive concave term. The positivity-preserving property and the unique solvability of the proposed numerical scheme are theoretically justified, utilizing the singular nature of the logarithmic term as the phase variable approaches the singular limit values. An unconditional energy stability analysis is standard, as an outcome of the convex-concave decomposition technique.