Layer-by-layer (LbL) immobilization of DNA aptamers in the realm of electrochemical detection of heavy metal ions (HMIs) offers an enhancement in specificity, sensitivity, and low detection limits by leveraging the cross-reactivity obtained from multiple interactions between immobilized aptamers and developed material surfaces. In this research, we present a LbL approach for the immobilization of thiol- and amino-modified DNA aptamers on a Ag-incorporated cobalt-succinate metal–organic framework (MOF) (Ag@Co-Succinate) to achieve a cross-reactive effect on the electrochemical behavior of the sensor. The solvothermal method was utilized to synthesize Ag@Co-Succinate, which was also characterized through various techniques to elucidate its structure, morphology, and presence of functional groups, confirming its suitability as a host matrix for immobilizing both aptamers. The Ag@Co-Succinate aptasensor exhibited extraordinary sensitivity and selectivity towards Hg(II) ions in electrochemical detection, attributed to the unique binding properties of the immobilized aptamers. The exceptional limit of detection of 0.3 nM ensures the sensor’s suitability for trace-level Hg(II) detection in various environmental and analytical applications. Furthermore, the developed sensor demonstrated outstanding repeatability, highlighting its potential for long-term and reliable monitoring of Hg(II).