Four kinds of alkyl salicylaldoxime (AS) were investigated to probe the effect of molecular structure on the extraction of Cu(II). With the augment of R groups, tert-octylsalicylaldoxime and nonylsalicylaldoxime have much stronger extraction ability for Cu(II) than salicylaldoxime and tert-butylsalicylaldoxime, which is consistent with the rise of hydrophobicity (Log P) of the extractants. The umbrella structure of the R group can endow tert-octylsalicylaldoxime with stronger steric-hindrance effect than nonylsalicylaldoxime, which results in the better separation efficiency of Cu(II) from Fe(III) for tert-octylsalicylaldoxime. The extraction ability of the extractants for Cu(II) is related to the hydrophobicity and molecular size, as predicted from quantum chemistry calculation.