In this work, we developed a novel strategy using fluorescent quantum dots (QDs) combined with molecularly imprinted polymers (MIPs) on three-dimensional (3D) origami paper-based microfluidic devices for specific recognition and sensitive detection of phycocyanin. This method can realize the liquid phase of QDs@MIPs being transferred to the solid-phase paper base and achieve easy portability for the analysis. Under optimal conditions, we successfully demonstrated the proposed paper@QDs@MIPs 3D microfluidic chip for the sensitive and selective detection of phycocyanin protein target in a simple and robust manner. Our results revealed that the method exhibited a dynamic response to phycocyanin in the range of 10−50 mg/L with a limit of detection of 2 mg/L. Importantly, this device could provide quantitative information very conveniently and show great potential to be further extended to the detection of other proteins or biomarkers for environmental and food safety research. KEYWORDS: paper-based microfluidic devices, molecularly imprinted polymers (MIPs), quantum dot, phycocyanin, fluorescence P hycocyanin, a blue-colored photosynthetic accessory pigment protein, is widely distributed in seawater, lake water, and algae microbes in drinking water, and has good survival ability. In addition, phycocyanin is a new desirable fluorescent marker with high stability and sensitivity and could be applied in biomedical and environmental fields. In the case of eutrophication of the water environment it often leads to algae bloom, causing serious deterioration of water quality. 1−3 The content of toxic substances produced by blue-green algae, including β-methylamino-alanine, 4 algal toxins, 5 nodularin, 6 and saxitoxin, 2,7,8 in the water is also increased and represents a serious threat to the safety of marine life and humans. Therefore, to protect the ecological balance of the environment, it is necessary to monitor and control the quantity of cyanobacteria. As its concentration can effectively represent cyanobacterial biomass, it can be used as an index of cyanobacteria outbreak and plays an important role in monitoring the marine ecological environment. 9 Current methods of detecting phycocyanin concentration mainly involve remote sensing methods, 10,11 UV, and fluorescence detection. 12,13 In addition, direct analysis of the water content of phycocyanin often requires separation and purification steps. Moreover, high cost and time-consuming methods add to the challenge, and development of a low-cost, fast, and efficient method for the detection of phycocyanin is urgently needed.Since the concept of microfluidic paper-based analytical devices (μPADs) was first proposed by the Whitesides group, 14 versatile μPADs have recently attracted increasing atten-