Tigriopus kingsejongensis, a copepod species, reported from the King Sejong Station, Antarctica, serves as a valuable food resource in ecosystems. Some copepods were temperature-sensitive in growth and post-embryonic development. We cultured T. kingsejongensis at three different temperatures (2°C, 8°C, and 15°C) in a laboratory to observe the alterations in the stool microbiome of copepods depending on the cultivation temperature and developmental stages. We observed copepod gut microbiome changes by increasing temperatures: a lower microbial diversity, a higher abundance of aquatic microbes, Vibrio, and a lower abundance of the psychrophilic microbes, Colwellia. Also, the copepod gut microbiome, according to the developmental stage, was changed: a lower microbial diversity in egg-attached copepods than nauplius at 8°C. We further analyzed three shotgun metagenomes from T. kingsejongensis stool samples at different temperatures and obtained 44 metagenome-assembled genomes (MAGs). We noted that MAGs of V. splendidus D contained glycosyl hydrolase (GHs) encoding chitinases and virulence factors with higher relative abundance at 15°C than at lower temperatures. These results that temperature and developmental stages affect the gut microbiome of copepods are helpful to understand the changes in the low-temperature adapted copepod with climate change.