In this paper, Mn(12)-based ordered honeycomb structures were successfully constructed from a simple solution casting process at high relative humidity through the modification of fatty acids to Mn(12) clusters. Mn(12)-fatty acid complexes maintain typical features of a single-molecule magnet as confirmed by IR spectra and magnetization hysteresis studies. Investigation of the effects of concentration, velocity of humid airflow, solvent, substrate, and alkyl chain length of the Mn(12) complex on the morphology of the honeycomb structures demonstrated wide generality and high reproducibility of the formation of Mn(12)-based self-organized honeycomb-patterned films. Both two-dimensional and three-dimensional honeycomb structures were obtained by adjusting the concentration of the complex solution. Mn(12)-based, honeycomb-patterned films maintain a paramagnetic response at room temperature, and thus give rise to a spatially distributed magnetic pattern on the substrate, which can be imaged by magnetic force microscopy. Importantly, the single-molecule magnetic property of the Mn(12) complex at low temperature is well maintained in the honeycomb-patterned film, which represents a promising outlook for high-density information storage and quantum computing applications.