The cotton-melon aphid, Aphis gossypii Glover, is a major insect pest worldwide. The wasp Lysiphlebia japonica (Ashmead) is the predominant parasitoid of cotton-melon aphids in north China. Parasitization has been reported to affect host lipids in several systems, but the lipid synthesis-related genes and transcription changes in the cotton-melon aphid-parasitoid interaction are not clear. In this study, 36 lipid synthesis-related genes were cloned and their transcription changes in parasitized aphids were studied by quantitative real-time PCR. In parasitized cotton-melon aphids, almost all key genes in the glycerolipid synthesis pathway were up-regulated, the rate-limiting enzyme diacylglycerol o-acyltransferase by 3.24-fold. The rate-limiting enzyme of the glycolytic pathway, pyruvate kinase, and the pace-making enzyme in citrate synthesis were 1.69-fold and 1.75-fold less in parasitized aphids than in unparasitized aphids, respectively. These results suggest increased glycerolipid synthesis in parasitized aphids but that citrate production from sucrose was decreased. Aconitate hydratase (aco), in the pathway that converts amino acids into citrate, was up-regulated. The number of fragments per kilobase per million mapped reads of the mitochondrial aco2 gene was only 4.6, whereas that of the cytoplasmic aco1 was 41.5, indicating that the citrate comes from amino acids in the cytoplasm of parasitized cotton-melon aphids.