‘Yali’ pear (Pyrus bretschneideri) is one of the most seriously varieties of pears affected by saline-alkali in China. The research aimed to study the fruit quality changes of pear under saline-alkali stress. It was found that the functional gene KEGG pathways and particular miRNAs’ target gene KEGG pathways were consistent in specific metabolites under saline-alkali stress. Combined with the correlation analysis of metabolites, three gradations were combined to form one closed loop, which perfectly resolved the effect of saline-alkali stress in fruit quality of ‘Yali’ pear from different levels. Callus induced from ‘Yali’ fruits 45 days after flowering was firstly introduced for mechanism research. The effects of saline-alkali factors on key differential metabolites, genes, miRNAs in ‘Yali’ pear fruit were investigated and researched respectively in callus.