Unique electronic, optical, and mechanical properties of molybdenum disulfide (MoS2) hold great potential and can be harnessed as a key component in novel applications in electronics, optoelectronics, high-performance sensing material, and photodetection. Carbon quantum dots (CDs) have attracted a great deal of attention because of their biocompatibility, high quantum yield, and tunable light-emission band for biological and photodetector applications. In this research, we used these two materials for the Hg2+ sensor. First, the sensing layer of MoS2 and carbon dots were prepared through sequential solvent exchange and hydrothermal methods, respectively; then, they were characterized. Since mercury, as one of the most harmful pollutants in water, has a significant negative impact on human health and its detection is of great significance, the proposed MoS2 field-effect transistor sensor functionalized with the DNA–CD hybrid was fabricated for the ultrasensitive detection of the Hg2+ ion in an aqueous environment. Specific T-rich DNA was used in the hybrid structure as the capture probe for label-free detection. The DNA-CD/MoS2 hybrid aptasensor was capable of the detection of Hg2+ in a concentration range from 1 aM to 10 pM with a detection limit of 0.65 aM. The effect of the DNA presence in Hg2+ detection was investigated, and the specificity of the aptasensor response to the Hg2+ ion was also evaluated in the presence of other common cations in the aqueous medium. Finally, the aptasensor was used for Hg2+ detection from samples of tap and mineral water with satisfactory results.