The structural properties and energetics of endohedral lithium and lithium ion doped Stone-Wales defected armchair and zigzag carbon nanocapsule systems have been explored theoretically. In order to investigate the effect of the defect on the systems, pristine capsule calculations have been also performed and presented briefly. The optimizations of the systems have been performed within the semi-empirical molecular orbital method at the PM3 level and the energies have been calculated with the density functional theory method using B3LYP exchange-correlation functional and 6-31G basis set. Furthermore, the thermodynamical properties for the optimized structures have been investigated by single-point energy calculations at PM3 level. The optimized geometries, total energies, some thermodynamical quantities, selected molecular orbital eigenvalues and dipole moments of the SW-defected and pristine C(5,5) and C(9,O) capsule systems have been reported.