To investigate the effect of pollination on the fruit quality of 'Dangshan Su' pear, 'Dangshan Su' was fertilized by the pollen of 'Wonhwang' ( Nakai.) (DW) and 'Jingbaili' ( Maxim.) (DJ). The analysis of primary metabolites was achieved through untargeted metabolomics, and the quantitative analysis of intermediate metabolites of lignin synthesis was undertaken using targeted metabolomics. The untargeted metabolomics analysis was performed via gas chromatography-mass spectrometry (GC-MS). The targeted metabolomics analysis was performed using ultra-high-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) under the multiple reaction monitoring (MRM) mode. The results showed that the metabolite content was significantly different between DW and DJ. Compared with that in DJ, the sugar and amino acid content in DW was higher and the fatty acid content was lower at 47 days after pollination (DAPs), and the sugar, amino acid, and fatty acid content in DW was lower at 63 DAPs. The intermediate metabolites of lignin synthesis were analyzed using the orthogonal partial least squares discriminant analysis (OPLS-DA) model, and the differential metabolites at 47 DAPs were -coumaric acid, ferulic acid, sinapaldehyde, coniferyl alcohol, and sinapyl alcohol. The differential significant metabolite at 63 DAPs was -coumaric acid. At 47 DAPs and 63 DAPs, the -coumaric acid level was significantly different, and the -coumaric acid content was positively correlated with lignin synthesis. The pollination pollen affects the quality of 'Dangshan Su' pear fruit through regulation of the sugar, amino acid, and fatty acid content; at the same time, regulating the levels of intermediate metabolites of lignin synthesis, especially the -coumaric acid content, to affect lignin synthesis ultimately affects the stone cell content and improves the quality of the pears.