A new direct method for determining the intermolecular structure of molecular assemblies in micropores using reverse Monte Carlo (RMC) simulation is proposed. The method gives the molecular configuration in an adsorption phase using experimental X-ray diffraction profiles and an assumed pore structure. This method has been applied to a carbon/water adsorption system to confirm previous results for the cluster formation of water in a hydrophobic space. The RMC method is a useful tool for estimating the pseudo-three-dimensional structures of molecular assemblies confined in pores from experimental data.