The cotton aphid, Aphis gossypii, is an important insect pest of many crops around the world, and it has developed resistance to a large number of frequently used insecticides. The sublethal effects of insecticides not only have an environmental risk to arthropods but also have the potential to promote resistance evolution. The sublethal effects (inhibitory or stimulatory) are influenced by many factors, such as the type of insecticide, sublethal concentrations, pest species, and others. In this study, the sublethal effects of sulfoxaflor and acetamiprid on A. gossypii were compared using two field-collected populations. The results show that sulfoxaflor was more toxic than acetamiprid against A. gossypii in both populations, the LC50 concentrations of acetamiprid and sulfoxaflor were 6.35 and 3.26 times higher, respectively, for the Jinghe population than for Yarkant. The LC25 concentration of acetamiprid significantly reduced adult longevity and fecundity in exposed adults (F0) of the Jinghe population, but it had no significant effects on these factors in Yarkant. Similar inhibitory effects were found in the F1 and F2 generations, but the biological traits in the Yarkant population were significantly reduced when the parents (F0) were exposed to LC25 of acetamiprid, whereas the changes in the Jinghe population were not significant. However, sublethal sulfoxaflor showed a stimulatory effect on A. gossypii in the F0 and F1 generation; the adult fecundity and longevity of the F0 generation were significantly higher in Jinghe, while the biological traits of the F1 generation were obviously higher in Yarkant. In the F2 generation, the r and λ were significantly higher in Jinghe; meanwhile, these biological traits were reduced in Yarkant. These results indicate that sulfoxaflor and acetamiprid had different sublethal effects on A. gossypii that varied by generation. In addition, we speculate that the genetic background and the resistance levels of A. gossypii may also influence the sublethal effects. Our findings are useful for assessing the overall effects of sulfoxaflor and acetamiprid on A. gossypii.