Phelipanche aegyptiaca Pers. is a holoparasitic plant that causes tremendous losses of agricultural crops worldwide. The initiation and development of the haustoria (special intrusive organs) is a key step in the growth of parasitic plants. The initiation of haustorium is largely dependent on haustorium-inducing factors (HIFs) secreted from host roots. Although HIFs of many semi-parasitic plants have been identified and reported, HIFs of the obligate parasitic plant P. aegyptiaca are largely unknown. This work demonstrated that the root exudates of the host plant Cucumis melo L. contain allelochemicals displaying haustorium-inducing activity on P. aegyptiaca germinating seeds, and there are significant differences in the induction effects of the resistant and susceptible C. melo cultivars of P. aegyptiaca (KR1326 and K1076). Ultra-performance liquid chromatography–mass spectrometry (UPLC-MS/MS) technology was used to identify and analyze the metabolites in root exudates of KR1326 and K1076. Cluster and PCA analyses showed significant differences between the metabolites in the KR1326 and K1076 root exudates. The determination of the haustorium induction effects of some metabolites screened from the differential metabolites indicated that scopoletin, quercetin, IAA, and DMBQ had relatively high haustorium induction activity. The results provide clues for finding HIFs of obligate parasitic plants and shed new light on the control of P. aegyptiaca by regulating haustorium development.