Many aphids can adapt on plants of differential resistance levels, but molecular interactions underlying host plant utilization and shift of aphids are still not well understood. Here, we sequenced the transcriptome and compared global gene expression profiles of Sitobion avenae (Fabricius) feeding on wheat (i.e., the susceptible plant) and barley (i.e., the resistant plant). In total, 65,200 high-quality unigenes were identified from the merged transcriptomes, and 861 of them were differentially expressed. Relative to their expression on barley, all differentially expressed P450 (cytochrome 450 monooxygenase) genes (e.g., SavCYP6A13, SavCYP4C1, and SavCYP4G15) in S. avenae on wheat were upregulated, suggesting the significance of P450s in xenobiotic metabolism for this aphid on wheat. For S. avenae on barley, some genes encoding for ATP-binding cassette (ABC) transporters (e.g., ABCG1, ABCG4, ABCB7, and ABCA5) and UDP-glucuronosyltransferases (UGTs; e.g., UGT2B1 and UGT2C1) showed a dramatic increase in expression, suggesting that ABC transporters and UGTs could be critical for detoxification metabolism in S. avenae on barley. In addition, the expression for nearly all differentially expressed proteases was upregulated for S. avenae on barley, reflecting xenobiotic challenges facing S. avenae on resistant barley. Thus, various detoxification and other defense-related genes (e.g., proteases and oxidases) showed highly inducible transcript regulation, suggesting great adaptive potential for S. avenae on different plants. All the abovementioned genes will be prime candidates for further studies of molecular interactions underlying host plant use and specialization in this aphid. Our results provide insights into aphids' defenses against variable phytochemicals, and the molecular basis underlying aphid-plant interactions as well.