Background: Fast emerging and increasing insecticide resistance in Asian tiger mosquito, Aedes albopictus brings alarm to the dengue epidemic over the world. The genetic and transcriptional sequencing has greatly advanced our understanding of the molecular basis for this crucial adaptation, but less is known about the regulation of insecticide resistance physiology at the metabolomic level. Methods: We captured the relative abundance of 17 amino acids and 34 AcylCNs in the 3rd to 4th instar larvae of three geographically close strains of Ae. albopictus, including a laboratory insecticide susceptible strain (Foshan) and two field deltamethrin-resistant strains (Yuexiu/Baiyun), as well as a laboratory induced deltamethrin-resistant (R18) and its parental insecticide susceptible strains (R0) to characterize their amino acids and acylcarnitines (AcylCNs) profiles by LC-MS/MS spectrometry. Results: Heatmap and PCA analysis of amino acids and AcylCNs profile indicated a clear separation of Foshan from Yuexiu/Baiyun populations, as well as a partly overlapping between Yuexiu and Baiyun populations. All strains were abundant in five amino acids (Pro, Val, Arg, Glu, His) and two AcylCNs (C0, C2). Five amino acids (Tyr, Cit, Pro, Thr, Gly) were significantly higher, while four amino acids (His, Val, Glu, Ala) were obviously lower in Yuexiu strain than Baiyun population. R18 displayed a differential amino acid and AcylCNs profile from its parental R0 strain. Conclusion: This study displayed a distinction of amino acids and AcylCNs profiles between insecticide-resistant and geographically or genetically-close insecticide-susceptible strain of Ae. albopictus, suggesting a possible application of amino acids and AcylCNs profiles for rapid diagnosis of deltamethrin resistance in Ae. albopictus in the future.