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<br>Display Omitted<br>• The effect of organic sample solvents in SCX mode were systematically studied. • Organic sample solvents affect the separation efficiency in SCX mode seriously. • Elution strength of organic solvents affect efficiency of later-eluted analyte. • Retention of organic solvents affected efficiency of earlier-eluted analyte. • The results can be used for the optimization of SCX methods.<br>This study investigated the influence of organic sample solvents on separation efficiency of basic compounds under strong cation exchange (SCX) mode. The mixtures of acidic aqueous solution and organic solvent such as acetonitrile, ethanol, methanol and dimethyl sulfoxide (DMSO) were tested as sample solvents. For later-eluting analytes, the increase of sample solvent elution strength was responsible for the decrease of separation efficiency. Thus, sample solvents with weak elution strength could provide high separation efficiencies. For earlier-eluting analytes, the retention of organic sample solvents was the main factor affecting separation efficiency. Weakly retained solvents could provide high separation efficiency. In addition, an optimized approach was proposed to reduce the effect of organic sample solvent, in which low ionic solvent was employed as initial mobile phase in the gradient. At last, the analysis of impurities in hydrophobic drug berberine was performed. The results showed that using acidic aqueous methanol as sample solvents could provide high separation efficiency and good resolution (<b>R</b> > 1.5).