Objective To study the effect of Propylthiouracil and Methimazole to liver function in hyperthyroidism patients. Methods 106 patients with hyperthyroidism who were admitted to Department of Internal Medicine of the Fourth People's Hospital of Wenling City from January 2010 to January 2013 were divided into group A and B by random number table. The initial dose of Methimazole was 30 mg/d, and the initial dose of Propylthiouracil was 300 mg/d. The dose of Methimazole and Propylthiouracil was reduced to 5-10 mg/d and 50-100 mg/d according to patient's condition respectively. The time of treatment was two years, the changes of liver function after treatment were compared between the two groups. Results The incidence rate of liver injury in group B(26.42%) was significantly higher than that in group A(11.32%)(P 0.05), but the happiness time of liver injury in group A [(18.74±7.68) d] was significantly more earlier than that in group B(41.65±8.27) d(P 0.05). The main manifestation of liver injury by Propylthiouracil was the increasing of serum alanine aminotransferase(78.57%), while the main manifestation of liver injury by Methimazole was the increasing of bilirubin(66.67%), which showed the different characters of indexes in liver injury. But there was no significant difference of liver injury between the two groups(P 0.05). Conclusion The liver injury by Methimazole happens more easily than that by Propylthiouracil, but the time of liver injury by Methimazole is little earlier than that by Propylthiouracil. The liver injury by Methimazole and Propylthiouracil is almost mild, the main manifestation of liver injury by Propylthiouracil is the increasing of serum alanine aminotransferase and the main manifestation of liver injury by Methimazole is the increasing of bilirubin.