Synthesizing a bimetallic metal-organic framework (MOF) by combining different MOFs into one hybrid material can lead to arising properties from the synergic heterostructure units while the properties of the individual MOFs are incorporated. In this work, bimetallic CuZr-MOFs were obtained through the MOF-on-MOF technique and exploited as a scaffold for the immobilization of aptamer on the surface of the electrode to form an electrochemical aptasensor for detecting miR-21, a biomarker for cancer diagnosis. The characterization results indicated that the crystalline features, chemical structure, and surface morphology of CuZr-MOFs could be regulated by alternating the order in which the organic linkers and metal precursors are added. The synthesized CuZr-MOF provided a relatively high surface area, large pore size, and strong affinity for aptamer strands, which could increase the number of aptamer strands immobilized on the surface of the modified electrode. The fabricated aptasensor displayed an excellent sensing performance with ultra-high sensitivity for the detection of miR-21, giving a significantly low detection limit of 0.45 zM as obtained by square-wave voltammetry within the wide detection range of 1 zM to 1 pM. The aptasensor also exhibited excellent selectivity, stability, admissible reproducibility, and accurate target detection in human serum. Therefore, according to the promising results, the fabricated aptasensor has a strong potential for early and sensitive diagnosis of miRNA-related diseases.