Nanoparticle deposition by drying of colloidal suspension in thin micro-porous architectures has attracted a lot of attention in scientific research as well as industrial applications. However, the underlying mechanisms of such three-dimensional (3D) deposition are not yet fully revealed due to the complexity of the co-occurring processes of two-phase fluid flows, phase change and mass transport. Consequently, the control of 3D nanoparticle deposition remains a challenge. We use a combined experimental and numerical approach to achieve controlled 3D nanoparticle deposition by drying of colloidal suspension in two pillar-based thin micro-porous architectures. By the design of pillar layout, rectangular-spiral and circular-spiral deposition configurations are obtained globally. By varying the surface wettability, vertically symmetric and sloped nanoparticle depositions can be achieved locally. While the numerical modeling reveals the mechanisms of liquid internal flow, as well as the impact of local drying rate on nanoparticle transport, accumulation and final deposition, the experimental results of deposition configurations validate the controlling strategies. This combined experimental and numerical work provides a framework to achieve desired 3D nanoparticle deposition in thin micro-porous architectures, with a thorough understanding of the underlying mechanisms of two-phase fluid flows, phase change and mass transport.