Abstract: 【Objective】 To explore the possible impacts of mineral elements and amino acids on rough-skin formation in Korla fragrant pear by comparing the differences o mineral elements and amino acids in rough-skinned fruits and normal fruits. 【Methods】 Inductively coupled plasma mass spectrometry (ICP-MS) and ultra-high performance liquid chromatography-mass spectrometry (UHPLC-MRM-MS/MS) techniques were used to detect the types and contents of mineral elements and amino acids in normal and rough-skinned fruits o Korla fragrant pear fruits collected from 15-year-old pear trees growing in an orchard in Korla (Xinjiang, China). 【Results】 The principal component analysis was carried out on the mineral elements and amino acids. A total of 14 mineral elements and 23 amino acids were detected in different types of fruits of Korla fragrant pear, among which 10 mineral elements and 19 amino acids were differentially accumulated in two types of fruits. In addition to boron (B) and silicon (Si), the contents of the other 8 elements (Na, Mg, P, K, Ca, Mn, Cu) in normal fruits were significantly higher than those in rough-skinned fruits with the fold-changes ranging from 0.70 to 3.17-fold. The contents of 19 differential accumulated amino acids in rough-skinned fruits were significantly higher than those in normal fruits, with the fold-changes ranging from 1.11 to 6.61-fold. Two principal components (PC) were extracted from principal component analysis (PCA) of these 14 mineral elements. Rough-skinned fruit samples and normal fruit samples were separated in the PC plot. Among them, Ca, K and Na had higher PC₁ correlation scores, while Se, Cu and B had higher PC₂ correlation scores. The elements with higher comprehensive scores in both PC₁ and PC₂ were Ca, Mn, K, etc. Similarly, two PCs were extracted from PCA of 23 amino acids, of which 4-hydroxyproline (4-hyp), ornithine (Orn) and histidine (His) had higher PC₁ correlation scores, and serine (Ser), glutamic acid (Glu) and 3-methyl-histidine (3-mehis) had higher PC₂ correlation scores. The amino acids with higher comprehensive scores in both PC₁ and PC₂ were threonine (Thr), alanine (Ala) and 4-Hyp. 【Conclusion】 The mineral elements and amino acids were differentially accumulated between two types of fruits. Differential accumulation of the mineral elements (Ca, Mn and K) and amino acids (Thr, Ala and 4-Hyp) with higher comprehensive scores might be one of the main reasons for the phenotypic differences between the rough-skinned and normal fruits.