The long time evolution of structural hierarchy in cross-linked natural rubber, i.e., cis-polyisoprene, was investigated in uniaxially stretched and partially retracted state using real time birefringence, optical microscopy, and wide angle X-ray scattering techniques. During the deformation, the needlelike domains that contain highly oriented crystals develop in the stretching direction. The constrained holding of these samples up to 14 days results in the development of additional crystals adjacent to original needlelike domains exhibiting lower orientation. Further holding up to 47 days results in lateral overgrowths of lamellar crystals emanating from these oriented crystals. Growth branching was found to be increasingly suppressed with the long-term crystallization that lead to the formation of two-dimensional crystals that grew the longest. Slight retraction after stretching results in a higher crystalline orientation with lower crystallinity due to retraction-induced melting of crystalline regions with lower orientation. The population of lateral lamellar overgrowths on oriented crystals was found to be larger in these stretched and retracted samples than the samples subjected to stretching only. Temperature dependent WAXS analysis of these crystallites in stretched and stretched-retracted samples indicates that the crystals with differing perfection and tilt angle with respect to the stretching direction melt earlier than their more perfectly aligned counterparts.