The development of simple, low-cost, and specific detection method for mercury (Hg(II)) ions in aqueous media using matrix-assisted laser desorption ionization mass spectrometry (MALDI-MS) is a challenge due to matrix interferences and acidity that destroy weak interactions. Herein, a new binary matrix consists of mefenamic acid, and thymine (T) is applied for simple and specific detection of Hg(II) in aqueous solution and blood sample. Mass spectra show metal-to-ligand ratio of 1:2 (Hg(II):T) in which Hg(II) ions are bound to two T molecules and two water molecules, i.e., [Hg(T)2(H2O)2]. The method is simple and fast, and requires cheap reagents. In addition, the spectra show extremely specific signals for Hg(II) ions and insignificant signals in case of other competing metal ions. The concept of our protocol can be applied for other metals. The new matrix may be used for the analysis of small molecules with minimal interferences peaks.