This work reported a label-free electrochemical aptasensor based on bimetallic ZnNi metal–organic framework (MOF) microspheres for highly efficient detection of adenosine (AD). Three ZnNi MOFs with different morphologies were prepared by regulating the molar ratio of Zn2+ to Ni2+ (1:1, 1:2, and 1:3) in the preparation processes. The ZnNi MOF (1:2)-based aptasensor displayed excellent sensing performance toward AD compared with ZnNi MOF (1:1) and ZnNi MOF (1:3)-based ones due to its higher electrochemical activity and stronger binding interaction between the aptamer strands and hierarchically nanostructured hollow microspheres. The proposed aptasensor exhibited a low detection limit of 20.32 fg·mL−1 for AD within a wide linear range from 0.0001 to 100 ng·mL−1. This aptasensor also showed excellent selectivity, acceptable reproducibility, high stability, good regenerability, and favorable applicability for AD detection in human serum. The remarkable biosensing performance was primarily attributed to the strong adsorption interactions of Ni2+ to aptamers, special morphology of materials, and the synergistic effect of Zn2+/Ni2+ in MOF matrixes. The rational construction of bimetallic ZnNi MOFs provided a promising sensing platform for sensitive detection of AD and further, showed great potentials in clinic diagnosis.