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 oil 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.