Purification of ultra-low-concentration malodorous gases from community and factory is a worldwide hot topic. Although adsorption is one of the most effective methods, seldom reports purified malodorous gas with a concentration lower than 1 ppm. In this work, metal (Zn, Al, Cu, Cr, Ce, Mn, and Fe) exchanged ZSM-5 are synthesized, and applied in removing 0.01 ppm of methyl mercaptan (MM), which is a typical malodorous gas. Cu-exchanged ZSM-5 shows the longest breakthrough time for MM removal among all metals. In addition, the zeolite is regenerable for MM purification. In order to make clear the most effective topological structures for Cu2+ localizations, Cu-exchanged X, Y, and ZSM-5 zeolites are compared in investigations of breakthrough time and topological structures. As a result, Cu-exchanged ZSM-5 shows the longest breakthrough time of 213 min. Moreover, removal efficiencies of various Cu2+ localizations follow the order of n-membered ring (n ≥ 8) ≪ double 6 ring ≈ 6-membered ring < 5-membered ring. A shorter-chain ring configuration creates a confinement effect, which makes the adsorption easier between Cu2+ and ultra-low-concentration MM. The main results this work help to develop and understand effective adsorbent for super clean emissions.