Rheological techniques reveal valuable information on the process behaviour of polymer melts. Moreover, structural information like molar mass distribution, degree of cross-linking or branching as well as crystallization effects are related to the rheological behaviour of polymeric systems.This paper explains the rheological and morphological behaviour of impact modified PBT/PTT blends based nanocomposites. Impact modified PBT/PTT blends based nanocomposites have been prepared by melt blending. ULDPE-g-GMA was used as an impact modifier for PBT and PTT polymeric matrix. It has been observed from results that the storage modulus, loss modulus and complex viscosity of the nanocomposites increased with the incorporation of organoclay (OMMT). Addition of organoclay to polymer matrix increased the storage modulus by several orders of magnitude and alters the shear thinning behaviour at low frequencies. Compositions having 5 wt % of organoclay shows high value of the storage modulus, loss modulus and complex viscosity. Moreover, storage modulus (G’) and loss modulus (G”) of impact modified 75/25 PBT/PTT (NA3) and 50/50 PTT/PBT (NB3) blends based nanocomposites with 5 wt % organoclay loading increased more significantly at lower frequency range relative to other compositions. PBT/PTT blends based nanocomposites followed a strong shear thinning flow behaviour and decreased with increasing shear rates or frequency. This change in behaviour showed a solid like behaviour and it is related to the morphological changes. The Complex viscosity of neat PBT, neat PTT and impact modified PBT and PTT decreased with increasing frequency because of the shear thinning behaviour. The morphology of PBT/PTT blends and its nanocomposites has been confirmed by FEG-SEM microscopy. FEG-SEM micrographs revealed that the clay layers are uniformly dispersed in PBT/PTT blends.