Polymer-based nanocomposites emerged in the 1960s as a groundbreaking approach to advanced materials. By incorporating robust, durable, and multifunctional nanomaterials into a polymer matrix, the performance of nanocomposites has significantly surpassed that of the base polymers. However, over the past six decades, the challenges of achieving uniform nanomaterial dispersion and the resulting non-uniform properties have impeded further progress in this field. Here, we present a polymer-based nanocomposite with highly dispersed nanomaterials, achieved through aerosol-jet-based multi-material three-dimensional (AM3D) printing. This method allows precise programming of the nanocomposite's composition, structure, and dispersity. Numerical simulations in the design of AM3D printing system facilitate the avoidance of interfacial compatibility issue among heterogeneous aerosols, enabling distributed printing without nanomaterial agglomeration. As a result of this high level of dispersion and distribution, the 3D structured nanocomposite exhibits a uniform dielectric constant and low dielectric loss across the entire printed area. This work establishes an engineering framework for defectfree nanocomposites and significantly expands the range of polymer-based multi-material nanocomposite that can be designed and manufactured with complex architectures. One-Sentence Summary: Aerosol-jet-based multi-material 3D printing enables highly dispersed nanomaterials in the polymer-based nanocomposite.