Forty-one apple samples from 7 geographical regions and 3 botanical origins in China were investigated. A total of 29 volatile compounds have been identified by flash GC E-nose. They are 17 esters, 5 alcohols, 3 aldehydes, 1 ketone, and 3 others. A principal component analysis was employed to study the relationship between varieties and volatiles. A partial least squares discriminant analysis (PLS-DA), stepwise linear discriminant analysis (SLDA), and decision tree (DT) are used to discriminate apples from 4 geographical regions (34 apple samples) and 3 botanical origins (36 apple samples). The most influential markers identified by PLS-DA are 2-hexadecanone, methyl decanoate, tetradecanal, 1,8-cineole, hexyl 2-butenoate, (Z)-2-octenal, methyl 2-methylbutanoate, ethyl butyrate, dimethyl trisulfide, methyl formate, ethanol, S(-)2-methyl-1-butanol, ethyl acetate, pentyl acetate, butyl butanoate, butyl acetate, and ethyl octanoate. From the present work, SLDA reveals the best discrimination results in geographical regions and botanical origins, which are 88.2% and 88.9%, respectively. Although machine learning DT is attempted to classify apple samples, the results are not satisfactory.