The intestinal metabolites of Tibetan sheep play a vital role in the integrated regulation of the host and the microbe-gut-brain axis. The current study sought to investigate the characteristics of alterations in rectal metabolites and their functional implications during the cold and warm seasons in Tibetan sheep. A cohort of 12 ewes, approximately 1 week ± 1 month in age, exhibiting good body condition and a similar genetic background, was selected for metabolomic analysis of rectal contents collected during the warm season (August) and the cold season (December). The findings revealed significant differences in the rectal microbial metabolites of Tibetan sheep between the two seasons (P < 0.05), with a total of 476 differential metabolites identified in the positive ion mode (148 up-regulated and 328 down-regulated) and 383 differential metabolites in the negative ion mode (135 up-regulated and 248 down-regulated). These differential metabolites were mapped to 12 KEGG metabolic pathways (P