A novel series of thiosemicarbazone derivatives having 1,3-dioxoisoindole core were synthesized from the reaction of N-(1,3-dioxoisoindolin-2-yl)aminothiocarbohydrazide (3) with a variety of aldehydes and ketones. Their geometrical and conformational isomers were investigated based on the analysis of their 1HNMR and 13CNMR spectra. The thiosemicarbazones were found to exist in the more stable structure III with an E configuration and a syn, syn disposition of both NH protons around the C=S bond. However, compounds 5b and 9c were existed as a mixture of E (major) and Z (minor) stereoisomers with a syn, syn conformation of both NH protons around the C=S bond as in structure III and VI, respectively. On the other hand, the thiosemicarbazones 9e,f and 15 derived from p-chloro-, p-bromoacetophenone and cyclopropylmethyl ketone 14 showed different behavior. They existed in solution of DMSO-d6 as a mixture of E (major) and Z (minor) geometrical isomers with syn, syn and, anti, anti disposition of both NH protons as in structure III and IV, respectively. Dehydrative cyclization of compounds 5b–g, i, 9a–d and 15 with acetic anhydride afforded only one stereoisomer of the hybrid heterocycles of the dioxoisoindole and thiadiazoline rings 16a–l as confirmed by 1H and 13C NMR spectra. DFT calculations revealed the extrastability of the E isomer relative to the Z one 5b, d and 15 as representative examples. The relative energies are small (5.1–5.8 kcal/mol) which further confirm their coexistence in solution.