Shiitake mushroom have been shown to have health benefits including lowering plasma lipids and preventing body weight gain. However, their underlying mechanisms are largely unknown. The study aim was to assess the potential underlying mechanism of Shiitake mushrooms in lowering plasma triacylglycerol (TAG) in rats fed a high fat diet (HFD). Forty Wistar rats were divided into control group were given HFD and treatment group were fed HFD, enriched with Shiitake mushroom powder at a low dose (LD-M): 0.7%, medium dose (MD-M): 2%, or high dose (HD-M): 6% (wt:wt) for six weeks. Diets were isocaloric containing ~50% energy from fat. After six weeks’ dietary intervention, the rats were sacrificed, and blood and tissue samples were collected. The HD-M group showed a significantly higher ratio of liver weight to 100 g body weight (p < 0.05), a more severe hepatic steatosis marker, such as hepatocyte ballooning (p < 0.0001), and more liver triacylglycerol content than LD-M and MD-M (p < 0.05). HD-M also showed a significantly decreased ratio of phosphatidylcholine (PC) to phosphatidylethanolamine (PE) compared to HFD (p < 0.05), however, there were no differences compared to HD-M and MD-M. Our results also showed a positive association between the dosage, liver TAG, and liver ballooning histology. A negative association was found between the mushroom dosage and the ratio of liver PC to PE. This study showed the mechanism of how high-dose Shiitake mushroom (HD-M) prevents obesity by increasing TAG accumulation in the liver, rather than adipose tissue.