To make full use of young pear fruit thinned from the trees for optimal fruit load during cultivation, this study explored the nutritional diversity in young fruit of seventy-nine different pear varieties, focusing on their bioactive compounds. Our results showed significant variability in total phenolic content (TPC), total flavonoid content (TFC), and antioxidant activity of pear varieties. The TPC values ranged from 0.317 ± 0.051 mg GAE/g to 0.0054 ± 0.021 mg GAE/g FW; the highest TPC value has been found in Lixian new bapan, mulberry pear, and red pear varieties, while the lowest value has found in yaqing, weining fragrant pear and apple pear varieties. Similarly, the TFC values demonstrated substantial differences, with Lijiang sesame pear (0.16 ± 0.01), Lixian new bapan (0.13 ± 0.04), and Xiangyuan (0.13 ± 0.02) pear exhibiting the highest flavonoid content. Antioxidant activity, assessed using the Ferric Reducing Antioxidant Power (FRAP) assay, varied significantly, indicating diverse phytochemical profiles across the varieties. HPLC analysis showed that the high value of bioactive compounds is chlorogenic acid (17.86 ± 4.5), arbutin (2.57 ± 0.3), Epicatechin (1.57 ± 0.27), rutin (0.04 ± 0.03) and ferulic acid (0.30 ± 0.04) found in the mulberry pear variety. Molecular docking studies revealed that chlorogenic acid, Epi-catechin, Rutin, and Ferulic acid showed strong affinity towards proteins such as Nrf2, NF-κB, and iNOS, suggesting potential health benefits. These findings provide valuable insights for breeders, nutritionists, and the food industry, emphasizing the importance of the nutritional quality of pear fruits, and their recycling utilization in the production practice.