Position of substituents (R1 = H and R2, R3 = H, F, CnHn+1) on malonaldehyde has been changed to amplify its intramolecular hydrogen bonding (IHB) interaction. Results show that π-conjugated substituents at R3 position cause increase of IHB energies of the substituted malonaldehydes. Then, amplification of the IHB interaction in malonaldehyde with C20H21 group at R3 position was verified. Thus, polyethylene chains influence on resonance-assisted hydrogen bond (RAHB) of malonaldehyde and can form malonaldehyde-polyene materials with improved properties. Then, hydrogen bond (HB) interaction of formaldehyde with the substituted malonaldehydes without RAHB ring was studied and HB interaction energies calculated. The HB interaction energies have linear relation with intermolecular hydrogen bond length (dHB). A procedure was employed to estimate IHB energies of the substituted malonaldehydes using the mentioned relation and intramolecular hydrogen bond length (dIHB). Relation between geometrical parameters, spectroscopic data, topological properties, and molecular orbital descriptors with the estimated IHB energies were surveyed. Moreover, IHB energies of the current system were estimated using some quantum chemistry methods to validate the data and find more consistent method with the proposed viewpoint. Results indicated that the estimated IHB energies using proposed procedure have good correlations with other methods. Also, energy decomposition of the IHB interactions in the substituted malonaldehydes was performed using a new method and results showed that electrostatic term has major contribution in the IHB energies.