Small-for-size graft injury is characterized by portal venous hypertension and loss of intracellular homeostasis early after transplant. The long-term alteration of sinusoidal microcirculatory hemodynamic state remains unknown. A syngeneic rat orthotopic liver transplantation model was developed using small-for-size grafts (35% of recipient liver weight) or whole grafts (100% of recipient liver weight). Graft survival, portal pressure, liver function, hepatocellular apoptosis as well as morphological changes (by light microscopy and electron microscopy) were assessed. Sinusoidal microcirculatory hemodynamics was examined by intravital fluorescence microscopy. Although portal hypertension lasted only for 1 h after performance of small-for-size liver transplantation, a sustained microcirculatory disturbance was accompanied by dramatic reduction of sinusoidal perfusion rate, elevation of sinusoidal diameter as well as increase in the number of apoptotic hepatocytes during the first 7 days. These resulted in lower survival rate (50% vs. 100%, P = 0.012), higher level of liver function, and more severe morphological changes, which could induce small-for-size syndrome. In conclusion, persistent microcirculatory hemodynamic derangement during the first 7 days after reperfusion as well as transient portal hypertension is significant manifestation after small-for-size liver transplantation. Long-term microcirculation disturbance displayed as decrease of sinusoidal reperfusion area and increase of spread in functional liver mass seems to be the key factor for graft injuries.