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In most cases, three-dimensional paper-based microfluidic analytical devices (3D-μPADs) were fabricated manually by stacking or folding methods. For the first time, digital light processing stereolithography (DLP-SLA) 3D printing technology was adopted to automatically make 3D-μPADs. In the fabrication process, a printing pause was set between two layers to allow paper to be placed in the resin tank. The resin on the fresh paper spontaneously bonded to the former cured paper layer during curing, thus realizing the automatic bonding and alignment between different layers of paper and avoiding the human participation and errors as in stacking and folding methods. There was a gap between two vertical aligned flow paths, therefore the liquid did not flow spontaneously from the upper layer to the lower layer. Most of the fluid flow in 3D-μPADs was spontaneous or manually activated, which was not conducive to complex assays that require different regents to be delivered sequentially. Herein, we used an electric field or airflow to trigger the fluid flow and demonstrated the flow controllability by a proof-of-concept colorimetric assay. The limits of detection of glucose and albumin were 0.8 mM and 3.5 μM, respectively, which were sufficient for clinical requirements. Given the characteristic of flow controllability, we believe that the proposed 3D-μPADs have great potential to make paper-based complex assays automated and programmable.