This study successfully integrates acoustic patterning with the Two-Photon Polymerization (TPP) process for printing nanoparticle–polymer composite microstructures with spatially varied nanoparticle compositions. Currently, the TPP process is gaining increasing attention within the engineering community for the direct manufacturing of complex three-dimensional (3D) microstructures. Yet the full potential of TPP manufactured microstructures is limited by the materials used. This study aims to create and demonstrate a novel acoustic field-assisted TPP (A-TPP) process, which can instantaneously pattern and assemble nanoparticles in a liquid droplet, and fabricate anisotropic nanoparticle–polymer composites with spatially controlled particle–polymer material compositions. It was found that the biggest challenge in integrating acoustic particle patterning with the TPP process is that nanoparticles move upon laser irradiation due to the photothermal effect, and hence, the acoustic assembly is distorted during the photopolymerization process. To cure acoustic assembly of nanoparticles in the resin through TPP with the desired nanoparticle patterns, the laser power needs to be carefully tuned so that it is adequate for curing while low enough to prevent the photothermal effect. To address this challenge, this study investigated the threshold laser power for polymerization of TPP resin (Pthr) and photothermal instability of the nanoparticle (Pthp). Patterned nanoparticle–polymer composite microstructures were fabricated using the novel A-TPP process. Experimental results validated the feasibility of the developed acoustic field-assisted TPP process on printing anisotropic composites with spatially controlled material compositions.