Designing and developing a reliable method for the detection of potential biomarker molecules are crucial for the early prevention and diagnosis of diseases. In this study, we present a novel functionalized metal–organic framework material (MOF-808) that is developed to construct ratiometric fluorescence sensing platforms (Eu/CDs@MOF-808) for the detection of adenosine triphosphate (ATP) and uric acid (UA). The fluorescent probe Eu/CDs@MOF-808 prepared through the in-situ encapsulation of fluorescent carbon dots (CDs) within the structure of MOF-808 exhibits excellent optical properties. Additionally, rare earth ions (Eu3+) are incorporated into the CDs@MOF-808 using a post-synthetic modification strategy. The presence of ATP significantly enhances the characteristic peak of carbon dots (CDs) at 440 nm, while the peak of Eu3+ at 614 nm remains relatively unchanged. Furthermore, the concentration of ATP exhibits a strong linear relationship with the ratiometric fluorescence intensity (F440/F614) in the concentration range of 0.5–450 μM, with a detection limit of 0.22 μM. Notably, the addition of uric acid (UA) to this fluorescence sensing platform leads to a marked reduction in the characteristic peak intensity of Eu3+, which results in a satisfactory linear relationship between the ratiometric fluorescence intensity and UA concentration in the concentration ranges of 0.04–300 μM and 300–650 μM, with a detection limit of 0.04 μM. Additionally, the fluorescent sensor has been successfully applied for the detection of ATP and UA in real serum and urine samples.