This study reported a novel biosensor based on the nanocomposite of zirconium metal-organic framework (Zr-MOF, UiO-66) embedded with silver nanoclusters (Ag NCs) using the carcinoembryonic antigen (CEA)-targeted aptamer as template (AgNCs@Apt@UiO-66). The synthesized AgNCs@Apt@UiO-66 nanocomposite not only possesses good biocompatibility, active electrochemical performance, and strong bioaffinity, but also can be dispersed to form two-dimensional nanocomposite with nanoscale thickness. As such, the use of the AgNCs@CEA-aptamer enables AgNC@Apt@UiO-66 with sensitive and selective detection capacity of trace CEA, further concurrently being exploited as scaffold for surface plasmon resonance spectroscopy (SPR) and electrochemical biosensors. The results showed that the proposed electrochemical AgNC@Apt@UiO-66-based aptasensor exhibits high sensitivity with a low detection limit (LOD) of 8.88 and 4.93 pg·mL deduced from electrochemical impedance spectroscopy and differential pulse voltammetry, respectively, within a broad linear range of the CEA concentration (0.01-10 ng·mL). Meanwhile, the developed SPR biosensor exhibited a slightly high LOD of 0.3 ng·mL within the CEA concentration of 1.0-250 ng·mL. Both the electrochemical and SPR aptasensors displayed high selectivity, good reproducibility, stability, acceptable regenerability, and applicability in real human serum samples. These results proved that the proposed aptamer-targeted Zr-MOF nanocomposite can be utilized in multiple-functionally biosensing, further promoting the potential application of Zr-MOF-related nanomaterials in clinical diagnosis.