The spinyhead croaker (Collichthys lucidus) is a commercially important fish species, which is mainly distributed in the coastal regions of China. However, little is known about the molecular regulatory mechanism underlying reproduction in C. lucidus. A de novo transcriptome assembly in brain, liver, ovary and testis tissues of C. lucidus was performed. Illumina sequencing generated 60,322,004, 57,044,284, 60,867,978 and 57,087,688 clean reads from brain, liver, ovary and testis tissues of C. lucidus, respectively. Totally, 131,168 unigenes with an average length of 644 bp and an N50 value of 1033 bp were assembled. In addition, 1288 genes were differentially expressed between ovary and testis, including 442 up-regulated and 846 down-regulated in ovary. Functional analysis revealed that the differentially expressed genes between ovary and testis were mainly involved in the function of sexual reproduction, sex differentiation, development of primary male sexual characteristics, female gamete generation, and male sex differentiation. A number of genes which might be involved in the regulation of reproduction and sex determination were found, including HYAL and SYCP3 and BMP15. Furthermore, 35,476 simple sequence repeats (SSRs) were identified in this transcriptome dataset, which would contribute to further genetic and mechanism researches. De novo transcriptome sequencing analysis of four organs of C. lucidus provides rich resources for understanding the mechanism of reproductive development of C. lucidus and further investigation of the molecular regulation of sex determination and reproduction of C. lucidus.