A density functional theory (DFT) is developed in three-dimensional nanoconfined space and applied for H-2 storage in metal-organic frameworks. Two different weighting functions based on the weighted density approximation (WDA) are adopted, respectively, for the repulsive and attractive contributions to the excess free energy. The Carnahan-Starling equation and a modified Benedicit-Webb-Rubin equation are used to calculate the excess free energy of uniform fluid. To compare with DFT predictions, grand canonical Monte Carlo simulations are carried out separately. For H-2 adsorption in MOF-5 and ZIF-8, the isotherms predicted from the DFT agree well with simulation and experiment results, and the DFT is found to be superior to the mean-field-approximation (MFA)-based theory. The adsorption energies and isosteric heats predicted are also in accord with simulation results. From the predicted density contours, the DFT shows that the preferential adsorption sites are the corners of metal clusters in MOF-5 and the top of organic linkers in ZIF-8, consistent with simulation and experimental observations.