'Xenia' is the terminology and biology of direct, or immediate, pollen effects on seeds and fruits. In this study, we found that the pollination of 'Jinsha' pomelo (JS) with pollen from Grapefruit (GR) and 'Majia' pomelo (MJ) led to significant differences in the seed numbers and primary metabolite (soluble sugar and amino acid). In pollinated pistils, the differences in the number of pollen tubes entering the embryo sac and the content of cytokinin components at 5 d post-pollination between the two pollen sources might be the important factor contributing to the discrepancies of seed trait and further affected fruit quality. In addition, joint analysis result of metabolomics and transcriptomics showed that the down-regulated expression of genes in the sucrose and starch metabolism pathways, glycolysis pathway and amino acid metabolism pathway of JS × MJ fruit compared to those of JS × GR fruit might also be resulted in an increase in the content of fructose and glucose and a decrease in the content of a large number of free amino acid components. This study revealed the reasons for the changes in seed and fruit characteristics induced by the xenia effect under two different pollen sources, and the hub genes novel.155 (HK), Cg2g040280 (bglX), Cg4g020710 (ISA), and Cg3g021210 (P4HA) were obtained by co-expression network analysis.