The invention relates to a heteroatom-containing organic microporous material as well as preparation and an application thereof. The structural general formula of the heteroatom-containing organic microporous material is as shown in the specification, wherein R is independently selected from one of hydrogen, a hydrophobic group, a hydrophilic group, a chiral group, an ester group, a cyano group, an amino group and a sulfhydryl group. The preparation method comprises the following steps: (1) synthesizing a dehydrobenzene derivative through Sonogashira reaction and Suzuki coupled reaction by taking m-bromoiodobenzene or 2-bromine-4-iodine-pyridine as an initial raw material, and then synthesizing a precursor through trimerization reaction catalyzed through cobalt octacarbonyl; (2) preparing the heteroatom-containing organic microporous material by carrying out Scholl reaction which takes ferric trichloride as an oxidizing agent on the obtained precursor. The heteroatom-containing organic microporous material disclosed by the invention can be used for preparing energy environment-friendly materials which store gases and absorb the hydrogen, carbon dioxide, methane and nitrogen oxides in the environment and has the advantages of good optical property, simple preparation method and excellent property.