To understand how internal flow structures manifest themselves in the global heat transfer, we study the correlation between different flow modes and the instantaneous Nusselt number ($Nu$) in a two-dimensional square Rayleigh-Benard convection cell. High-resolution and long-time direct numerical simulations are carried out for Rayleigh numbers between $10^{7}$ and $10^{9}$ and a Prandtl number of 5.3. The investigated Nusselt numbers include the volume-averaged $Nu_{text{vol}}$, the wall-averaged $Nu_{text{wall}}$, the kinetic energy dissipation based $Nu_{text{kinetic}}$, and the thermal energy dissipation based $Nu_{text{thermal}}$. The Fourier mode decomposition and proper orthogonal decomposition are adopted to extract the coherent flow structure. Our results show that the single-roll mode, the horizontally stacked double-roll mode, and the quadrupolar flow mode are more efficient for heat transfer on average. In contrast, the vertically stacked double-roll mode is inefficient for heat transfer on average. The volume-averaged $Nu_{text{vol}}$ and the kinetic energy dissipation based $Nu_{text{kinetic}}$ can better reproduce the correlation of internal flow structures with heat transfer efficiency than that of the wall-averaged $Nu_{text{wall}}$ and the thermal energy dissipation based $Nu_{text{thermal}}$, even though these four Nusselt numbers give consistent time-averaged mean values. The ensemble-averaged time trace of $Nu$ during flow reversal shows that only the volume-averaged $Nu_{text{vol}}$ can reproduce the overshoot phenomena that is observed in the previous experimental study. Our results reveal that the proper choice of $Nu$ is critical to obtain a meaningful interpretation.
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