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Game theory—the scientific study of interactive, rational decision making—describes the interaction of two or more players from macroscopic organisms to microscopic cellular and subcellular levels. Life based on molecules is the highest and most complex expression of molecular interactions. However, using simple molecules to expand game theory for molecular decision-making remains challenging. Herein, we demonstrate a proof-of-concept molecular game-theoretical system (molecular prisoner’s dilemma) that relies on formation of the thymine⁻Hg2+⁻thymine hairpin structure specifically induced by Hg2+ and fluorescence quenching and molecular adsorption capacities of cobalt oxyhydroxide (CoOOH) nanosheets, resulting in fluorescence intensity and distribution change of polythymine oligonucleotide 33-repeat thymines (T33). The “bait„ molecule, T33, interacted with two molecular players, CoOOH and Hg2+, in different states (absence = silence and presence = betrayal), regarded as strategies. We created conflicts (sharing or self-interest) of fluorescence distribution of T33, quantifiable in a 2 × 2 payoff matrix. In addition, the molecular game-theoretical-system based on T33 and CoOOH was used for sensing Hg2+ over the range of 20 to 600 nM with the detection limit of 7.94 nM (3σ) and for determination of Hg2+ in pond water. Inspired by the proof-of-concept for molecular game theory, various molecular decision-making systems could be developed, which would help promote molecular information processing and generating novel molecular intelligent decision systems for environmental monitoring and molecular diagnosis and therapy.