This study aimed to investigate the effects and mechanism of selenium-enriched kiwifruit (Se-Kiwi) on lipid-lowering and liver protection in hyperlipidaemic mice induced by consuming a long-term high-fat diet. Selenium-enriched cultivation can significantly improve the contents of vitamins and functional elements in kiwifruits, especially vitamin C, selenium, and manganese, thus enhancing the activity of antioxidant enzymes in Se-Kiwi. Se-Kiwi can significantly improve the activity of antioxidant enzymes in the liver of hyperlipidaemic mice, restore the liver morphology of mice close to normal, reduce the fat content in the liver, and inhibit the accumulation of abdominal fat cells. Meanwhile, the expression levels of inflammation-related factors (TNF-α and NF-κB) and lipid synthesis related genes (SREBP-1c and FAS) are inhibited at the gene transcription and protein expression levels, and the expression levels of energy expenditure related genes (PPAR-α and CPT1) are increased, resulting in lipid reductions and liver protection. In conclusion, our results indicate that the protective mechanism of Se-Kiwi on high-fat diet mice is associated with enhancing the activity of antioxidant enzymes, reducing the degree of the inflammatory reaction, inhibiting the fat synthesis, and accelerating body energy consumption.