We present an optimal rate convergence analysis for a second order accurate in time, fully discrete finite difference scheme for the Cahn–Hilliard–Navier–Stokes (CHNS) system, combined with logarithmic Flory–Huggins energy potential. The numerical scheme has been recently proposed, and the positivity-preserving property of the logarithmic arguments, as well as the total energy stability, have been theoretically justified. In this paper, we rigorously prove second order convergence of the proposed numerical scheme, in both time and space. Since the CHNS is a coupled system, the standard ℓ∞(0,T;ℓ2)∩ℓ2(0,T;Hh2) error estimate could not be easily derived, due to the lack of regularity to control the numerical error associated with the coupled terms. Instead, the ℓ∞(0,T;Hh1)∩ℓ2(0,T;Hh3) error analysis for the phase variable and the ℓ∞(0,T;ℓ2) analysis for the velocity vector, which shares the same regularity as the energy estimate, is more suitable to pass through the nonlinear analysis for the error terms associated with the coupled physical process. Furthermore, the highly nonlinear and singular nature of the logarithmic error terms makes the convergence analysis even more challenging, since a uniform distance between the numerical solution and the singular limit values of is needed for the associated error estimate. Many highly non-standard estimates, such as a higher order asymptotic expansion of the numerical solution (up to the third order accuracy in time and fourth order in space), combined with a rough error estimate (to establish the maximum norm bound for the phase variable), as well as a refined error estimate, have to be carried out to conclude the desired convergence result. To our knowledge, it will be the first work to establish an optimal rate convergence estimate for the Cahn–Hilliard–Navier–Stokes system with a singular energy potential.