Methyl orange (MO) is a widely used organic dye in industrial chemical production and biomedical research. However, its presence also poses potential risks to the environment and public health. The current MO sensing methods face numerous challenges such as low detection efficiency, expensive equipment, and complex operation. In this study, we propose a detection scheme based on heterostructure upconverting nanocrystals (UCNCs), where BaYF5:20Yb/0.5 Tm@SrYF5 UCNCs function as the energy donor, while the organic molecule methyl orange acts as the electron acceptor to quench the fluorescence emission band. The brightness and UC efficiency of NCs is significantly improved by engineering the interfacial strain. Specifically, the UC intensity of the BaYF5:Yb/Tm@SrYF5 core/shell NCs, exhibited a substantial increase of approximately 425-fold compared to that of the core NCs. The detection limit is measured to be about 0.25 μM, which is better than most reported fluorescence sensors. These results highlight the significant application prospects of fluorescence detection technology in the field of environmental safety.