Miscibility and morphology of poly(ethylene 2,6-naphthalate)/poly(trimethylene terephthalate)/poly(ether imide) (PEN/PTT/PEI) blends were investigated by using a differential scanning calorimeter (DSC), optical microscopy (OM), wide-angle X-ray diffraction (WAXD), and proton nuclear magnetic resonance (1H-NMR). In the ternary blends, OM and DSC results indicated immiscible properties for polyester-rich compositions of PEN/PTT/PEI blends, but all compositions of the ternary blends were phase homogeneous after heat treatment at 300 °C for more than 30 min. An amorphous blend with a single Tg was obtained in the final state, when samples were annealed at 300 °C. Experimental results from 1H-NMR identified the production of PEN/PTT copolymers by so-called “transesterification”. The influence of transesterification on the behaviors of glass transition and crystallization was discussed in detail. Study results identified that a random copolymer promoted the miscibility of the ternary blends. The critical block lengths for both PEN and PTT hindered the formation of crystals in the ternary blends. Finally, the transesterification product of PEN/PTT blends, ENTT, was blended with PEI. The results for DSC and OM demonstrated the miscibility of the ENTT/PEI blends.