In comparison with metallic thermoelectric films, oxide films with artificial nanodefects have been seldom studied. And there has been no report on the incorporation of islandshaped organic nanoparticles. We describe a new approach to introduce nanometer-sized phonon scatterers in aluminum-doped ZnO (AZO) thermoelectric thin films-concurrent multi-beam multi-target-pulsed laser deposition and the matrix-assisted pulsed laser evaporation (MBMT-PLD/MAPLE). The approach was used to make nanocomposite thin films of AZO matrix with evenly dispersed poly(methyl methacrylate) (PMMA) nanoparticles. The introduction of the nanoparticles enhanced phonon scattering with consequent decrease of thermal conductivity by 20%. The electrical conductivity did not decrease after the addition of the second phase, as it would be predicted by WiedemannFranz law, but improved by 350% over pure AZO film. The thermoelectric figure of merit of the nanocomposite film became twice that of the pure AZO film. Taking advantage of room-temperature deposition, optimized AZO nanocomposite films are expected to be used in real applications, such as thin film modules deposited on flexible polymeric substrates for ubiquitous harvesting of the waste heat.