The invention provides a paper-based device based on a moving valve and molecular imprinting technology, and a manufacturing method and application thereof. The manufacturing method comprises the following steps of pattern design, chip fabrication, electrode construction on a paper base, chip connection, synthesis of a functionalized molecularly imprinted polymer layer, electrochemical polymerization, and elution of template molecules. The device is used for analysis and detection of biomarkers in serum samples. The invention provides a paper-based device based on moving valve and molecular imprinting technology, a manufacturing method and application thereof, and provide a novel device for clinically detecting biomarkers. The device is used for in-situ synthesis of biomarker molecularlyimprinted polymer, forms a clinical application method, creates a new strategy for antibody-free biomarker analysis, realizes the entire process from device fabrication to test result output on the paper-based device, and is economical, portable, high in speed.