Artemia nauplii is an important live food item for marine fish and crustaceans. However, the HUFA content of Artemia from different origins varies greatly and is generally low. Compared with other species or strains, Artemia cysts in Tibet salt lakes have very high HUFA content, which may be related to their unique living conditions. This study determined the effects of dietary HUFA (P. tricornutum and C. zofingiensis), salinity (4%, 8%, and 12%), and temperature (14 °C, 19 °C, and 24 °C) on the HUFA accumulation of Lagkor Co Artemia tibetiana after 14-day culture, in comparison with Great Salt Lake Artemia franciscana. The results showed that the HUFA profile of Artemia was closely related to the dietary HUFA level, and the low temperature and low salinity could significantly increase the ARA, EPA, and DHA content. PCA results showed that the fatty acid distribution patterns of the two Artemia species were mostly affected by dietary fatty acids, which were greater than those of temperature, salinity, and Artemia species. RNA-seq analysis and qRT-PCR verification revealed that low temperature and low salinity could promote the gene expression of fatty acid binding protein gene, long chain fatty acid elongase, and desaturase, suggesting these genes may be involved in the process of HUFA accumulation in A. franciscana. In conclusion, diet is a key factor affecting HUFA accumulation in Artemia, while low temperature and low salinity led to higher HUFA retention. The findings of this study provide a reference for revealing the mechanism of HUFA synthesis and metabolism of Artemia, and to develop the Artemia products with high HUFA content through manipulation of culture conditions.