An ultrasensitive controlled release system electrochemical aptasensor (CRSEA) has been developed for supersensitive determination of mercury ions (Hg2+), using gold nanoparticle-linked specific single-stranded DNA (Au NPs-ssDNA) as a molecular gate and mesoporous silica nanocontainers (MSNs) as containers. MSNs have a rich porous structure, thus entrapping the toluidine blue (TB) molecules inside. It is worth noting that Hg2+ binds to the ssDNA with multiple thymine (T) and induces the ssDNA to form a hairpin structure, which makes the separation of the Au NPs-ssDNA from the MSNs. Eventually, the stored TB molecules were released from MSNs. The electron transfer signals of TB were detected stably by a differential pulse voltammetry (DPV) detection method, which are correlated with the concentration of Hg2+. Therefore, the wide linear range (10 pM-100 μM) and low limit of detection (2.9 pM) were obtained, and the system also displayed an apparent electrochemical signal response in real sample detection and showed a promising possibility in actual monitoring.