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The codling moth, <i>Cydia pomonella</i> L. (Lepidoptera, Tortricidae), is a serious invasive pest of pome fruits. Currently, <i>C. pomonella</i> management mainly relies on the application of insecticides, which have driven the development of resistance in the insect. Understanding the genetic mechanisms of insecticide resistance is of great significance for developing new pest resistance management techniques and formulating effective resistance management strategies. Using existing genome resequencing data, we performed selective sweep analysis by comparing two resistant strains and one susceptible strain of the insect pest and identified seven genes, among which, two (glycine receptor and glutamate receptor) were under strong insecticide selection, suggesting their functional importance in insecticide resistance. We also found that eight genes including <i>CYP6B2</i>, <i>CYP307a1</i>, <i>5-hydroxytryptamine receptor</i>, <i>cuticle protein</i>, and <i>acetylcholinesterase</i>, are potentially involved in cross-resistance to azinphos-methyl and deltamethrin. Moreover, among several P450s identified as positively selected genes, <i>CYP6B2</i>, <i>CYP4C1</i>, and <i>CYP4d2</i> showed the highest expression level in larva compared to other stages tested, and <i>CYP6B2</i> also showed the highest expression level in midgut, supporting the roles they may play in insecticide metabolism. Our results provide several potential genes that can be studied further to advance understanding of complexity of insecticide resistance mechanisms in <i>C. pomonella</i>.