The ripe Gannan navel oranges have an appealing aroma, but few studies have reported the changes of these aromatic substances during the growth of navel oranges. In this study, changes of aroma components in Gannan navel orange from 119 to 245 days after flowering were systematically studied using headspace solid-phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC–MS) coupled with multivariate analysis, including principal component analysis (PCA) and partial least squares discriminant analysis (PLS-DA). A total of 43 and 54 aroma components were identified in pulp and peel of navel orange, respectively. The odor active value (OAV) results indicated that 14 substances were the key aroma components during the growth of navel orange. Among them, the contribution of linalool, β-myrcene and limonene were the highest. The multivariate statistical analysis further confirmed that 14 and 18 compounds could be used as key markers to distinguish the pulp and peel at different growth stages, respectively. Results from this study contributed to a better understanding of the dynamic variation and retention of aroma compounds during navel orange growth, and have great potential for industrial application.