In this work, a microfluidic paper-based fluorescent sensor device was constructed for quantitative detection of microRNA (miRNA) and determination of the expression of folate receptor (FR) on the cell surface. It is worth pointing out that simultaneous detection of two biomarkers in cancer was achieved through dynamic self-assembly of T-shaped duplex structure. T-shaped duplex structure can respond to specific triggers and convert to an output due to the conformation changes, it is meaningful to fabricate T-shaped duplex structure into powerful biosensors that can monitor chemical stimuli. Moreover, lamellar MnO2 nanosheets were synthesized, which exhibited excellent quenching ability via adsorbed fluorophore-labeled ssDNA, but the adsorption of the dsDNA was significantly lower than ssDNA because of the shielding of nucleobase pairs by the phosphate groups. This newly designed biosensor provided a sensitive detection of miR-21 from 0.01 to 5.0 fM with a relatively low detection limit of 0.0033 fM. Besides, the present sensing system has a detection of FR in the range from 2.0 to 30.0 ng/mL with the detection limit of 0.667 ng/mL. As biological markers for disease diagnosis, the detection of FR and miRNA will provide a new approach and therapeutic tool for early clinical diagnosis.