Through investigating the spin-dependent charging energy of nanoscale systems, we introduce a new concept of intrinsic molecular magnetocapacitance (MC). In molecules and nanosize quantum dots that undergo a spin state transition, the MC can be as high as 12%. First-principles calculations demonstrate that in a number of nanoscale systems, the quantum capacitance is highly sensitive to the system spin and charge states. In single molecule junctions, one can exploit molecular MC through the Coulomb blockade effect by modulating the bias voltage and applying an external magnetic field, which turns electron conductance on or off. Detailed analysis on molecular nanomagnet Mn(3)O(sao)(3)(-)(O(2)CMe)(H(2)O)(py)(3) shows a 6% MC with a switching field of ~40 T. Its MC can be further enhanced to 9.6% by placing the molecule above a dielectric surface, opening up new avenues for novel nanoscale materials design. Under current experimental conditions, the predicted molecular MC effect can be probed without substantial difficulties.