Goose is a seasonal breeding animal. Its reproduction is regulated by hypothalamus-pituitary-gonad axis and also affected by environmental factors such as light and location. Zi-goose is characterized with long egg-laying period and high egg-laying potential and belongs to the long-day type of seasonal breeding. In this study, the regulation mechanism of different lighting on reproductive performance of Zi-goose by using metabonomics analysis technology. In addition, 1,481 differential metabolites were screened out totally. 583 differential metabolites were identification in hypothalamus of Zi-goose. 196 differential metabolites were identification in pituitary of Zi-goose. 692 differential metabolites were identification in ovary of Zi-goose. Under red light condition for 12 h, expression of 433 differential metabolites were down-regulated and expression of 150 differential metabolites were up regulated in hypothalamus of Zi-goose, expression of 125 differential metabolites were down-regulated and expression of 71 differential metabolites were up-regulated in pituitary of Zi-goose, expression of 355 differential metabolites were down-regulated and expression of 337 differential metabolites were up-regulated in ovary of Zi-goose. 33 differential metabolites were closely associated with 1,264 transcripts and 400 homologous genes of related enzymes in hypothalamus of Zi-goose. 15 differential metabolites were closely associated with 163 transcripts and 47 homologous genes of related enzymes in pituitary of Zi-goose. 55 differential metabolites were closely associated with 1,255 transcripts and 360 homologous genes of related enzymes in ovary of Zi-goose. It was confirmed that four metabolic pathways were closely related to light regulation of reproductive performance of Zi-goose, namely GnRH signaling pathway, prolactin signaling pathway, thyroid hormone synthesis and ovarian steroidogenesis. Typical differential metabolites of arachidonic acid, glucose-6-phosphate, progesterone, glutathione, oxidized glutathione, testosterone, deoxyepiandrosterone and their related protein genes would play an important role in light regulation of reproductive performance of Zi-goose.