Ovaries (O) are specialized tissues that play critical roles in producing oocytes and hormones. The crustacean hepatopancreas (H) is a metabolic organ that plays important functions including absorption, storage of nutrients and vitellogenesis during growth and ovarian development. However, genetic information on the biological functions of the crustacean ovaries and hepatopancreas are limited. This study compared the transcriptome in the ovary and the hepatopancreas of female P. trituberculatus fed two different diets containing 0% (SL0) and 4% soybean lecithin (SL4), respectively during the growth and ovarian maturation stages by Illumina HiSeq4000 sequencer. The differences between ovary and hepatopancreas of P. trituberculatus were also compared at transcriptional level. A total of 55,667 unigenes were obtained with mean length of 962 bps across the four treatment groups (SL0_O, SL4_O, SL0_H and SL4_H). In ovary, there were 257 differentially expressed genes (DEGs) between SL0_O and SL4_O, with 145 down- and 112 up-regulated genes in the SL4_O group. Candidate genes involved in ovarian development were detected in SL4_H group. In hepatopancreas, 146 DEGs were found between SL0_H and SL4_H, including 43 down- and 103 up-regulated genes in the SL4_H group. The specific DEGs were mainly involved with lipid related metabolism pathways, including fat digestion and absorption, PPAR signaling pathway and insulin resistance. 14,725 DEGs were found in the comparison between SL0_O and SL4_H, including 7250 up- and 7475 down-regulated genes in the SL4_H group. The specific DEGs were mainly involved with lipid (fat digestion and absorption, linoleic acid metabolism), hormone (steroid hormone biosynthesis, ovarian steroidogenesis, etc), and amino acid (phenylalanine metabolism, arginine biosynthesis, tyrosine) related metabolism pathways. Crabs fed the SL4 diet exhibited higher gene expression of cryptocyanin 1 (cc1), cryptocyanin 2 (cc2) and neuroparsin 1 (np1) in hepatopancreas and ovarian than those fed the SL0 diet, however, crab fed SL4 diet showed higher gene expression of fatty acid-binding protein 1 (fabp1), vitellogenin (vtg) and Delta-6 desaturase-like protein (fadsd6) in hepatopancreas than those fed the SL0 diet. Moreover, crabs fed the SL0 diet had lower gene expression of vtg, extracellular copper‑zinc superoxide dismutase (cuznsod) and estrogen sulfotransferase (ests) in ovary compared to those fed the diet containing 4% soybean lecithin. These results might provide important clues with respect to elucidating the molecular mechanisms underlying the regulation of phospholipid on the gonadal development and lipid metabolism of P. trituberculatus.