Marine microalgae have emerged as a significant source of health-promoting bioactive compounds, with Phaeodactylum tricornutum from the East Sea showing remarkable potential. This study aimed to isolate P. tricornutum along the East Sea coastline, particularly near Jeongdongjin Beach, and to assess its efficacy in combating obesity and associated metabolic disorders. Our analysis confirmed the presence of fucoxanthin-rich P. tricornutum, a marine diatom with unique bioactive properties. Through a 10-week regimen, oral administration of P. tricornutum extract to a high-fat diet-induced obesity mouse model resulted in a significant reduction in body weight gain, adiposity, cholesterol, and low-density lipoprotein levels. Furthermore, it notably alleviated the symptoms of non-alcoholic fatty liver disease, including hepatic lipid accumulation and fibrosis. These outcomes suggest that East Sea-derived P. tricornutum is an effective marine bioresource for managing obesity and its metabolic repercussions. This study highlights the therapeutic potential of marine microalgae in developing dietary supplements and natural health solutions and presents P. tricornutum as a potent anti-obesity agent with comprehensive metabolic benefits.