A novel electrochemical aptasensor based on a bimetallic organic frame-derived carbide nanostructure of Co and Ni (NiCo2O4@NiO) was prepared for rapid and sensitive enrofloxacin (ENR) detection of sheep and pork liver meats. The composite was fabricated by solvothermal and direct pyrolysis methods and dropped onto a modified electrode to improve the electron transfer efficiency. Furthermore, different techniques such as scanning electron microscopy and X-ray photoelectron spectroscopy were used to characterize the morphology and structure of the materials. Electrochemical impedance spectroscopy and cyclic voltammetry were used to evaluate the performance of the electrochemical sensor. As a result, the electrochemical aptasensor based on NiCo2O4@NiO exhibited excellent sensing performances for ENR with an extremely low detection limit of 1.67 × 10−2pg mL−1and a broad linear range of 5 × 10−2to 5 × 104pg mL−1, as well as great selectivity, excellent reproducibility, high stability and applicability. In addition, the relative standard deviation for real samples was in the range of 93.83 to 100.09% and 94.95 to 100.01% for sheep and pork liver. The results showed that the composite can be expected to greatly facilitate ENR detection and practical applications in harmful food due to the advantages of simple fabrication, controllable, large-area uniformity, environmental friendliness, and trace detection.