Pectin oligosaccharides (POSs) can not only be used as prebiotics to promote the growth of beneficial bacteria in the intestine but also can be used as natural food-borne antiglycation agents to inhibit the formation of advanced glycation end products (AGEs) in vitro, which is related to their structure, including molecular weight and galacturonic acid content. In this study, haw polysaccharides (HPSs) were isolated and purified, and POSs with high antiglycation activity in vitro were prepared. On this basis, the inhibitory effect of POSs on the formation of AGEs in infant formula milk powder was investigated. The results showed that no obvious inhibitory effect of POSs was found on the formation of AGEs in infant formula milk powder under accelerated storage at 25 °C and 45 °C. But, POSs showed a strong inhibitory effect on the formation of furosine, Nε-carboxymethyllysine (CML), Nε-carboxyethyllysine (CEL) and the total AGEs in infant formula milk powder under accelerated storage at 65 °C. In addition, POSs also had a strong inhibitory effect on the formation of lipid oxidation products but did not affect the formation of protein degradation products. Simultaneously, the cytotoxicity experiments using human umbilical vein endothelial cells showed that the infant formula milk powder supplemented with POSs had the lowest cytotoxicity compared to the blank control (BC) and GOS/FOS supplementation milk powder under accelerated storage at 65 °C, which may be related to the inhibitory effect of POSs on the formation of AGEs in infant formula milk powder. Furthermore, the in vitro fermentation experiments showed that the antiglycation process did not affect the prebiotic activity of POSs in infant formula milk powder.