Dwarf Interstocks Improve Aroma Quality of ‘Huahong’ Apple ( Malus × domestica )

‘Huahong’ is a popular apple cultivar because of its anti-browning properties and appealing aroma and flavor. It is mainly planted by grafting on dwarf interstocks in Northeast China. We investigated the different aroma profiles of apple fruits grown from six dwarf interstocks (‘CG24’, ‘SH38’, ‘SH3’, ‘MD001’, ‘Mac9’, and ‘CX5’) and from no interstocks (CK). A total of 55 VOCs were detected, including esters (25), aldehydes (14), alcohols (8), ketones (3), alkane hydroxyls (3), and acids (2). Among the VOCs, 48 were detected in the skin and 21 in the pulp. The skin of ‘Huahong’ apples had a strong sweet aroma, and the pulp was green with a subtle aroma. The dominant compounds (>5% of total content) in the skin were 2-methyl butyl acetate, hexyl 2-methyl butyrate, caproic acid butyl ester, hexanal, (Z)-2-heptene aldehyde, and 6-methyl-5-heptene-2-ketone, while in the pulp, they were 2-methyl butyl acetate, methanol, 2-methyl-1-butanol, hexanol, and hexane. Compared with CK, ‘SH38’, ‘MD001’, and ‘SH3’ interstocks had increased total aroma content, and ‘CX5’ and ‘CG24’ had suppressed aroma. The effects of interstocks on aroma were mainly reflected in skin. The VOC content ranged from 3297.52 to 9895.75 µg·kg −1 in skin, and from 748.62 to 1369.21 µg·kg −1 in pulp. PCA revealed that use of interstock ‘SH38’ mainly affected esters. ‘MD001’ affected hexane and 4-pentene-1-acetate; ‘Mac9’ and ‘SH3’ affected octanoic acid-2-methyl butyl ester, hexyl butyrate, and 2-methyl-1-butanol; and ‘CX5’ and ‘CG24’ had a greater impact on isoamyl propionate and 1-pentene-3-ol. Finally, ‘SH38’ had the highest principal comprehensive score. ‘SH38’ and ‘SH3’ interstocks resulted in significantly increased apple VOC content.