Self-organized microporous structures based on a series of surfactant-encapsulated polyoxometalate complexes (SECs) have been prepared by using ordered condensed droplets as a template. Among these structures, ordered honeycomb structures were obtained and characterized in detail by taking (DODA)(12)H[Eu(SiW11O39)(2)] (SEC-1) as an example. Optical microscope, atomic force microscopic, and scanning electron microscopic measurements confirmed the formation of three-dimensional microporous structure, in which the top surface shows a highly ordered honeycomb structure. As compared to common solvent-casting films, the corresponding honeycomb films are more hydrophobic and possess more ordered lamellar structures. Both the wettability and the size of SECs exert significant influence on the formation of microporous structures. The proper hydrophobicity of SECs was proposed to be an essential factor for the formation of honeycomb films, and large-sized SECs are favorable for the fabrication of highly ordered honeycomb structures. The conditions for the formation of different surface morphologies have been discussed in terms of the contact angle of SECs at the interface between water and chloroform, and a contact angle slightly greater than 90 degrees is found to be a prerequisite for the formation of honeycomb structures. The results reported in this paper not only help to further comprehend the mechanism of the formation of honeycomb structures, but also provide some guidance for the design of ordered microporous films based on organic/inorganic hybrid materials, exemplified by the organic/nanoparticle complexes.