Chinese fir (Cunninghamia lanceolata (Lamb.) Hook.) is the most important afforestation tree species in China because of its excellent timber quality and high yield. However, the limited availability of phosphorus in forest soils is widespread and has become an important factor in the declining productivity of Chinese fir plantations. Here we used the Illumina HiSeq™ 2000 DNA sequencing platform to sequence root, stem, and leaf transcriptomes of one-year old Chinese fir clones with phosphorus treatment. Approximately 236,529,278 clean reads were obtained and generated 35.47 G of sequencing data. These reads were assembled into 413,806 unigenes with a mean length of 520 bp. In total, 109,596 unigenes were annotated in the NR (NCBI non-redundant) database, 727,287 genes were assigned for GO (Gene Ontology) terms, information for 92,001 classified unigenes was assigned to 26 KOG (Karyotic Orthologous Groups) categories, and 57,042 unigenes were significantly matched with 132 KEGG (Kyoto Encyclopedia of Genes and Genomes) predicted pathways. In total, 49 unigenes were identified as exhibiting inorganic phosphate transporter activity, and 14 positive genes’ expression patterns in different phosphorus deficiency treatments were analyzed by qRT-PCR to explore their putative functions. This study provides a basic foundation for functional genomic studies of the phosphate transporter in Chinese fir, and also presents an extensive annotated sequence resource for molecular research.