Long-chain alkenones (LCAs) are important tools for paleotemperature reconstructions in lacustrine and marine environments. However, some neutral lipid compounds that co-elute with LCAs often occur in natural sediment samples, which seriously interferes with the identification and quantification of the LCAs. In this study, we report a new flash column chromatography based on silver(I)-dimercaptotriazine (Ag-DMT) functionalized silica material (≡Si-DMT-Ag) for purifying and isolating the individual LCAs from complex lake and marine sediment samples. Compared to silver(I)-mercaptopropyl (Ag-MP) functionalized (≡Si-(CH2)3-S-Ag) and silver nitrate (SiO2 + AgNO3) impregnated silica materials used by previous studies, the Ag-DMT stationary phase displays the best efficiency in removing co-eluting compounds (including wax ester, hopanoid, hopanoic acid, sterane, alkanoic acid, and some unknown compounds) from the LCAs in our study lake and marine sediment samples. The Ag-DMT material also shows its high retention capacity for the LCAs, probably due to a strong interaction of more positively charged silver sites on Ag-DMT with double bonds. Employing the Ag-DMT chromatography, we develop an optimal solvent elution scheme to efficiently isolate the individual LCAs with the same chain length but different numbers of unsaturation for their isotopic analysis in the future. Our study provides a highly effective method for eliminating co-eluting compounds and isolating individual LCAs for paleoclimate studies.