The synthesis of C2-symmetrical bis(β-enamino-pyran-2,4-dione) derivative 3 connected via 1,6-hexylene linker was reported for the first time. X-ray structures and Hirshfeld studies of the new bis- β-enamino-pyran-2,4-dione derivative 3 along with two structurally related pyran-2,4-dione derivatives 2a,b were discussed. A comparative analysis of the different intermolecular contacts affecting the crystal stability was presented. Generally, the H…H, O…H, and H…C interactions are common in all compounds and are considered the most abundant contacts. In addition, DFT calculations were used to compute the electronic properties as well as the 1H and 13C NMR spectra of the studied systems. All compounds (except 3) are polar where 2a (3.540 Debye) has a higher dipole moment than 2b (2.110 Debye). The NMR chemical shifts were calculated and excellent correlations between the calculated and experimental data were obtained (R2 = 0.93–0.94).