The cotton aphid (Aphis gossypii Glover) (Hemiptera: Aphididae) is a major pest of cotton (Gossypium hirsutum L.) grown in Xinjiang and is an agricultural pest found worldwide. With the extensive use of insecticides, A. gossypii in Xinjiang has developed high levels of resistance to a variety of insecticides. Afidopyropen is a new biogenic insecticide that is effective against insects with piercing-sucking mouthparts and has no cross-resistance with any commonly used insecticides in cotton fields. However, to our knowledge, the risk and stability of resistance of A. gossypii to afidopyropen and its detoxification enzymes under high selection pressure have not yet been elucidated. In this study, resistant A. gossypii specimens were selected with the cotton leaf-dipping method under laboratory conditions, and the realized heritability of A. gossypii resistance to afidopyropen was calculated using domain trait analysis. After 18 successive generations of selection for afidopyropen resistance, a resistant population with a median lethal dose (LC₅₀) of 9.006 mg/L was obtained; the resistance ratios had increased 23.033 times. The realized heritability was 0.063, and a 10-fold increase in resistance required only 20–26 generations when mortality was 60–80%. The 15th generation of the resistant strain had some resistance instability, and glutathione S-transferases played an important role in the detoxification metabolism of afidopyropen. The results of this study provide a basis for application of afidopyropen and management of A. gossypii resistance.