Multi-material vat photopolymerization (MMVPP) is an emerging additive manufacturing technology with great potential in biomedical engineering, soft robotics, electronics, and customized manufacturing, particularly where functional gradients and spatially varying material properties are essential. The capability to precisely control composition at the voxel level enables the fabrication of bioinspired structures and multifunctional components with tailored mechanical and functional performance. This study presents the conceptual design and development of a compact and commercially viable MMVPP system that addresses key challenges in current state-of-the-art technologies. A two-vat prototype printer was fabricated to demonstrate the feasibility of precise multi-material printing. Critical challenges, including resin compatibility, interfacial adhesion, and mechanical property optimization, were systematically investigated. Novel strategies such as variable layer height exposure control, overlapped layer printing, and optimized curing parameters were introduced to improve interfacial bonding and overall structural integrity. The proposed methods were validated through mechanical testing, confirming enhanced interface strength and material cohesion. The study also details system-level innovations, including efficient vat-switching mechanisms and process synchronization for rapid material transition. These advances establish foundational methodologies for reliable multi-material photopolymerization and expand the design space of photopolymer-based additive manufacturing. The results demonstrate MMVPP’s transformative potential to enable next-generation manufacturing of functionally graded and multi-material components with superior performance and design freedom.