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The origins of stereo- and face-selective Diels–Alder reactions of 5-substituted 1,3-cyclopentadienes (CP) with some dienophiles were elucidated by means of semiempirical PM5, DFT(B3LYP), and ab initio RHF methods. The activation energies by the improved PM5 and B3LYP/6-31+G(d) methods were in good agreement with the experimental results. We partitioned the activation energy (ΔEact) into diene deformation (ΔEdf-dien) and dienophile deformation (ΔEdf-dphil), and the diene–dienophile interaction (Eint) energies, in addition to the new intrinsic reaction coordinate (IRC) energy (ΔEirc) partitioning. Such analysis revealed the major factors in the determining endo/exo and syn/anti selectivities of the reactions of 5-substituted CP. The syn-selectivity of the 5-F-CP is explained by the lower ΔEact (2–3 kcal/mol) caused by relatively smaller ΔEdf-dien, which leads to slighter repulsion between the reactants. This low activation energy is inferred to be caused by the better second orbital interaction or intramolecular orbital interactions between the diene π and fluoro-substituent n orbital moieties, as well as by better intermolecular π–π orbital interactions between the diene-π and dienenophile-π moieties. On the other hand, the anti-selectivity of the methyl substituted CP mainly appears from bigger Edf-dien in the syn-isomer. A novel economical method of IRC energy partitioning to the reactants, TS intermediates and products is also introduced in order to verify the energy balance of other calculation methods and other reactions.