The effect of transesterification on the rheological property of poly(ethylene naphthalate)/poly(butylene tore-phthalate) (PEN/PBT) blends has been investigated. The melt viscosity of PEN/PBT blends decreased with increasing PBT content due to the relatively low melt viscosity of PBT as well as introducing ransesterification between PEN and PBT Further melt viscosity decrease was achieved by the thermal annealing which caused both the chain scission and the acceleration of transesterfication. Calcium stearate (CaST) was applied as a lubricant in order to lower the melt viscosity of PEN and it was found that CaST was acting as the catalyst of transesterification as well. In general, reactive melt blending of PEN and PBT by transesterification resulted in the decrease of molecular weight of PEN and PBT, as a result, the loss of mechanical properties in PEN/PET blend was inevitable.