Masson pine (Pinus massoniana) is primarily present within subtropical and tropical areas in China, and a number of these regions have a severe deficiency in inorganic phosphate (Pi). As a macronutrient, phosphorus plays a crucial role in plant development. Although several studies have documented the responses of masson pine to Pi starvation at a global level using RNA-Seq and comparative proteomic analyses, the detailed features in the roots that primarily respond to low Pi stress have not yet been studied. Our study examined the response of masson pine roots to a deficiency in Pi. Approximately 1117 unigenes were shown to respond to Pi deficiency by differential expression when analyzed using RNA-Seq. A total of 819 and 298 of these transcripts were up- and down-regulated, respectively. Several transporters including phosphate transporters (PHT1, PHO88), ABC transporters and metal transporters were identified. The ethylene response factor (ERF) was found to be the most abundant transcription factor. Analyses of these genes, including gene ontology enrichment and the KEGG pathway analysis, indicated that the metabolic processes are the most enriched under abiotic stresses, including Pi deficiency. This study provided abundant transcriptomic information to functionally dissect the response of masson pine roots to Pi deficiency. This will additionally aid to elucidate the biological regulatory mechanisms that the pines use to respond to low Pi stress.