Cadmium (Cd) is a highly toxic heavy metal element which has a long half-life and is difficult to degrade. Even at very low concentrations, it can cause great damage to fish. Peroxisome proliferator activated receptor-γ co-activator-1 (pgc1) is a transcriptional co-activator that coordinately regulates the activities of PPARγ, plays an important regulatory role in energy metabolism, mitochondrial biosynthesis, and antioxidative system in organisms. In this study, the cis-regulatory elements, sequence characteristics, evolutionary relationship, tissue expression characteristics of pgc1α and pgc1β gene promoter in Chinese perch, and the circadian rhythm of pgc1α and pgc1β genes in brain exposed to cadmium were analyzed. The results showed that NF-E2 and IRF1 binding sites existed in the promoter of pgc1α and pgc1β, and KLF9 binding sites existed in the promoter of pgc1β. Both pgc1α and pgc1β genes contained a complete LXXLL motif and RRM domain. Chinese perch pgc1α and pgc1β shared 51.6% and 59.7% homology with zebrafish and 41.5% and 28.4% homology with human homologous genes, respectively. The expression of pgc1α and pgc1β genes in Chinese perch has obvious tissue specificity, and are highly expressed in the brain, kidney, and heart. Under natural conditions, the expression of pgc1α and pgc1β in Chinese perch brain showed a trend of being high in the day and low in the night, and the peak phase of gene expression was ZT 7.07 h and ZT 8.25 h, respectively. The diurnal variation of pgc1α and pgc1β gene expression in Chinese perch brain was reduced and the amplitude was decreased under heavy metal cadmium stress. The peak phase of gene expression was advanced to ZT 3.71 h and ZT 5.65 h, respectively, indicating that cadmium exposure causes a significant disturbance on the circadian rhythm of pgc1α and pgc1β in Chinese perch brain.