Brain natriuretic peptide (BNP) is the preferred biomarker for clinical analysis, widely used in early screening and prognostic monitoring of cardiovascular and neurological diseases. Due to the low concentration and short half-life of BNP in the blood, its sensitive detection remains a challenge that must be overcome. With the rapid development of molecular diagnosis and point-of-care testing (POCT), developing a BNP biosensor with high sensitivity, good stability, accuracy, speed, and low-cost is of great significance for clinical applications and emergency diagnosis. However, BNP in human blood exists in various forms, and traditional fluorescence sensors may lead to overestimation of the concentration. In this work, we constructed an “on” fluorescent aptasensor based on competitive recognition strategy for quantitative detection of BNP, and built a fluorescence sensing detection system based on smartphone to achieve rapid on-site detection. We designed a specific aptamer labeled with carboxyfluorescein (FAM) with a simple structure and high biological affinity for selective capture of BNP, and utilized the large specific surface area and excellent fluorescence quenching effect of carboxylated graphene oxide (GO-COOH) as a carrier and quencher for the aptasensor. By optimizing experimental parameters such as aptamer and GO-COOH concentrations, as well as quenching/recovery time, linear sensitive detection of BNP was achieved in the concentration range of 0.01 ng/mL–10 ng/mL, with a detection limit as low as 10 pg/mL, good specificity, and excellent application potential in artificial serum spiking experiments. Additionally, a stable and sensitive fluorescence signal collection system has been developed to meet the needs of portable detection, breaking through the usage environment of traditional fluorescence detection equipment and filling the gap of portable fluorescence biosensing. In summary, we have creatively proposed a fluorescent aptasensor that enables rapid and sensitive detection of BNP and the development of low-cost fluorescent biosensors. The combination with POCT has shown broad application prospects and also provides some ideas for the fluorescence detection of other protein biomarkers.