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Aldehyde oxidase (AO) enzyme is known to oxidize aldehydes. One of the aldehydes, formaldehyde, is known to inhibit xanthine oxidase as it turns over. However, there is no reported data whether it behaves the same when it reacts with aldehyde oxidase. Similarly, the effect of chalcogen replacement on nucleophilic reaction and charge density distribution on the substituted analogs of formaldehyde and their behavior during catalysis has never been studied. Therefore, the research is intended to probe the most tractable substrate that interacts to the reductive half-reaction active site of AO. Therefore, a density functional theory of the B3LYP correlation functional formalism (DFT-B3LYP) methods was used to generate several parameters from the electronic structure calculations. Accordingly, the higher percentage (%) contribution to HOMO and energy barrier (kcal/mol) (0.099, -7.185040E+04) makes formaldehyde as the favored substrate for aldehyde oxidase, compared to thioformaldehyde (-0.245, -2.745113E+05) and selenoformaldehyde (-0.175, -1.529992E+06), respectively. In addition, the transition state structures for the active site bound to formaldehyde (ACT-FA), thioformaldehyde (ACT-THIO FA), and selenoformaldehyde (ACT-SELENO FA), respectively, were confirmed by one imaginary negative frequency (S-1) (-328.44, -430.266, and -624.854).