Scope Published data support that fish oil and algae oil rich in ω‐3 polyunsaturated fatty acids (PUFAs) protect against hyperlipidemia in mice. This study is aimed to explore the effects of fish oil and algae oil on high‐fat diet (HFD) induced circadian intestinal microbes dysregulation. Methods and Results Male C57BL/6 mice are randomly divided into four groups, which are fed a normal chow diet (CON), a HFD, a HFD supplemented with fish oil (FO), and a HFD supplemented with algae oil (AO), respectively, for 12 weeks. At the end of the experiment, mice are sacrificed at 12 h intervals with the first one at zeitgeber time 0 (ZT0) and the second at zeitgeber time 12 (ZT12). FO and AO groups ameliorate diet‐induced hyperlipidemia. The relative abundance of certain genera is improved in FO and AO groups according to 16S rRNA gene sequencing. The short‐chain fatty acids (SCFAs) producing bacteria Butyricimonas and some of the genera in the Lachnospiraceae recover to the normal circadian rhythm in both FO and AO groups. Conclusion The data show that FO and AO alleviate circadian gut microbiota dysregulation in mice caused by HFD, and support the further investigation of ω‐3 PUFAs as a dietary intervention strategy for the prevention of hyperlipidemia.