Recently, fabrication of metal micro-pattern has attracted a great attention. For such purpose, site-selective activation is crucial for metal deposition on a substrate, and it can be achieved through lithography, chemical vapor deposition and micro-contact printing. Here, we propose to control the activation point three-dimensionally (3D) through two-photon absorption (TPA) polymerization method, which leads to 3D site-selective deposition. Two types of photopolymer were prepared for deposition control of metal through electroless plating method. One was a commercially available resin, which is typically inactive to metal deposition. Another was a modified resin containing suitable functional groups for metal adhesion. We created a 3D polymer structure consisting of those two components by localizing each resin through TPA method. The fabricated structures were immersed in an electroless plating solution of silver. The partially silver coated sample was observed by a scanning electron microscope after washing and desiccation. Metal microstructure supported with polymer can be realized by 3D site-selective metal deposition. Therefore, it is a useful technique for 3D aligned metallic microstructures without any contacts each other.