Novel Bi2Te3/graphene quantum dots (Bi2Te3/GQDs) hybrid nanosheets with a unique structure that GQDs are homogeneously embedded in the Bi2Te3 nanosheet matrix have been synthesized by a simple solution-based synthesis strategy. A significantly reduced thermal conductivity and enhanced powder factor are observed in the Bi2Te3/GQDs hybrid nanosheets, which is ascribed to the optimized thermoelectric transport properties of the Bi2Te3/GQDs interface. Furthermore, by varying the size of the GQDs, the thermoelectric performance of Bi2Te3/GQDs hybrid nanostructures could be further enhanced, which could be attributed to the optimization of the density and dispersion manner of the GQDs in the Bi2Te3 matrix. A maximum ZT of 0.55 is obtained at 425 K for the Bi2Te3/GQDs-20 nm, which is higher than that of Bi2Te3 without hybrid nanostrucure. This work provides insights for the structural design and synthesis of Bi2Te3-based hybrid thermoelectric materials, which will be important for future development of broadly functional material systems.