In this study, the chemical compositions of Huanglongbing-symptomatic (HLB-SY) and Huanglongbing-asymptomatic (HLB-AS) Newhall navel oranges were comprehensively studied. Our results indicated that the orange juice of HLB-SY contained fewer amounts of TSS (total soluble solids), fructose, glucose, sucrose and Vc (vitamin C), while having more limonin and TA (titratable acidity) when compared to the respective one in HLB-AS juice, which was consistent with most of the previous reports. The hesperidin and didymin, however, were significantly (p < 0.05) less present in HLB-SY juice, with narirutin content being almost unchangeable, differing from the majority of earlier studies. On the contrary, the contents of primary flavonoids in HLB-SY peel, involving narirutin, hesperidin, didymin, 3,6,7,8,2′,5′-hexamethoxyflavone, nobiletin, 4′,5,6,7-tetramethoxyflavone, 3,3′,4′,5,6,7,8-heptamethoxyflavone and tangeretin, were significantly (p < 0.05) higher than those in HLB-AS peel. Meanwhile, when compared to the HLB-AS peel oil, the HLB-SY peel oil contained a significantly (p < 0.05) higher percentage of 4 monoterpenoids (sabinene, 3-carene, terpinolene, limonene-1,2-epoxide), 4 fatty aldehydes (octanal, nonanal, decanal, undecanal), and 3 alcohols (4-thujanol, linalool, α-terpineol), while showing significantly lower in the percentage of 5 terpene aldehydes (citronellal, geranial, neral, β-sinensal, α-sinensal), 3 sesquiterpenoids (valencene, β-cadinene, nootkatone), and limonene. The principal components analysis (PCA) was used to visualize the correlations amongst the variation of chemical compositions. The results presented here might be beneficial for the value-added utilization of HLB fruits.