In order to study the effects of Citrus Huanglongbing infection on the fruit qualities of Citrus reticulata cv. chachiensis, the differences of flavonoids and volatiles between the infected and normal fruits (180 days after full bloom) were compared with high performance liquid chromatography (HPLC) and gas chromatography-mass spectrometry (GC-MS). The results showed that contents of 4 polymethoxyflavones such as tangeretin and 39 volatiles including α-pinene and octanal were significantly increased in the infected peels while contents of 16 volatiles including N-methyl n-methylanthranilate and copaene significantly decreased. contents of 2 polymethoxyflavones such as nobiletin and 27 volatiles including D-limonene and β-linalool in the pulp were significantly decreased at the same time. It is indicated that infection of Huanglongbing may significantly affect the secondary metabolism in the peel and pulp of the Citrus reticulata cv. chachiensis, and thus change its bitterness and aroma quality, which may be related to its susceptibility defense response mechanism.