The aroma fraction of fresh fruits is a key factor to evaluate quality and acceptance or resistance of customers. Due to the limited sensitivity of current analytical methods, many important aroma components are unidentified in most studies of fresh fruit. In this work, the aroma compounds in the fresh navel orange were studied by multidimensional gas chromatography quadrupole time-of-flight mass spectrometry which can simultaneously achieve one-dimensional and comprehensive two-dimensional separation on only one instrument, with no need to change columns. As a result, a total of 97 volatile compounds were determined by comprehensive two-dimensional gas chromatography while only 44 compounds were identified by one-dimensional gas chromatography. The identified compounds, which account for 98.30% of the volatile chemicals present in the orange, include 10 aldehydes, 8 ketones, 22 alcohols, 12 esters, 11 hydrocarbons and 34 terpenes. D-limonene was shown to be the predominant compound in fresh navel oranges. The results show that comprehensive two-dimensional gas chromatography provided reliable and comprehensive information on the aroma compounds in fresh navel oranges.