Comparing gene expression among parasitic plants infecting different host species can have significant implications for understanding host-parasite interactions. Taxillus nigrans is a common hemiparasitic species in Southwest China that parasitizes a variety of host species. However, a lack of nucleotide sequence data to date has hindered transcriptome-level research on T. nigrans. In this study, the transcriptomes of T. nigrans individuals parasitizing four typical host species (Broussonetia papyrifera [Bpap] a broad-leaved tree species; Cryptomeria fortunei [Cfor] a coniferous tree species; Cinnamomum septentrionale [Csep] an evergreen tree species; and Ginkgo biloba [Gbil] a deciduous-coniferous tree species) were sequenced, and the expression profiles and metabolic pathways compared among hosts. A total of 40.06 Gb of clean sequence data were generated in nine cDNA libraries. These were de novo assembled into 293,823 transcripts with an N50 value of 1790 bp. A large number of differentially expressed genes (DEGs) were identified when comparing T. nigrans individuals on different host species: Bpap vs. Cfor (713 DEGs), Bpap vs. Csep (1219), Bpap vs. Gbil (1514), Cfor vs. Csep (1639), Cfor vs. Gbil (1722), and Csep vs. Gbil (1723). Three hundred and eighty-one unigenes were common to all six pairwise comparisons; these were primarily associated with carbohydrate metabolism and energy metabolism, as determined in a KEGG enrichment analysis. Specific involvements included: the TCA cycle, biosynthesis of secondary metabolites, carbon metabolism, biosynthesis of amino acids and glyoxylate/dicarboxylate metabolism. A total of 251 unique unigenes were also identified, specific to either the Bpap vs. Cfor (249 unigenes) or Csep vs. Gbil (two unigenes) comparisons; partial unigenes were associated with the plasma membrane, response to endogenous stimuli, ion binding, and organic hydroxy compound metabolic processes. These results provide a foundation for further explorations of the detailed molecular mechanisms involved in plant parasitism.