Moment equations were developed for partial filling CE systems, in which solute dissolution phenomena by spherical molecular assemblies or intermolecular interactions take place. Because experimental conditions of partial filling CE are divided into five categories on the basis of the magnitude relationship between the migration velocity of solute molecules and that of molecular assemblies or ligand molecules, the moment equations were systematically developed for each case by using the Einstein equation for diffusion and the random walk model. In order to demonstrate the effectiveness of the moment equations, they were applied to the analysis of partial filling CE behavior, which is correlated with dissolution phenomena of small solute molecules into spherical molecular assemblies as specific examples. Simulation results only in the case that the migration velocity of solute molecules is faster than that of molecular assemblies were represented in this paper. Detailed explanations about the derivation procedure of the moment equations and the simulation results in other cases can be found in the Supporting Information. The moment equations are theoretical bases for applying partial filling CE to the study on solute permeation kinetics at the interface of spherical molecular assemblies and on reaction kinetics of intermolecular interactions.