The medicinal plantCistanche deserticolaMa (Orobanchaceae) is a holoparasitic angiosperm that takes life-essential materials fromHaloxylon ammodendron(C. A. Mey.) Bunge (Amaranthaceae) roots. Although many experiments have been conducted to improve the quality ofC. deserticola, little attention has been paid to the host’s influence on metabolite accumulation. In this study, transcriptomic and metabolomic analyses were performed to unveil the host’s role inC. deserticola’s metabolite accumulation, especially of phenylethanoid glycosides (PhGs). The results indicate that parasitism byC. deserticolacauses significant changes inH. ammodendronroots in relation to metabolites and genes linked to phenylalanine metabolism, tryptophan metabolism and phenylpropanoid biosynthesis pathways, which provide precursors for PhGs. Correlation analysis of genes and metabolites further confirms thatC. deserticola’s parasitism affects PhG biosynthesis inH. ammodendronroots. Then we found specific upregulation of glycosyltransferases in haustoria which connect the parasites and hosts. It was shown thatC. deserticolaabsorbs PhG precursors from the host and that glycosylation takes place in the haustorium. We mainly discuss how the host resistsC. deserticolaparasitism and how this medicinal parasite exploits its unfavorable position and takes advantage of host-derived metabolites. Our study highlights that the status of the host plant affects not only the production but also the quality of Cistanches Herba, which provides a practical direction for medicinal plant cultivation.