Objective: To investigate the effects of methimazole and propylthiouracil on glucose and lipid metabolism, serum thyroxine, cystatin C and beta 2-microglobulin in patients with hyperthyroidism. Methods: 100 patients with hyperthyroidism diagnosed and treated in general surgical thyrid department in our hospital from September 2017 to September 2018 were divided into the control group and the observation group according to different treatment regimens, each 50 cases. Patients in the control group were treated with propylthiouracil, and those in the observation group treated with methimazole. Both groups were treated for consecutive 1 year. The clinical effects and adverse reactions of patients in the two groups were observed. [Low-density lipoprotein cholesterol LDL-C, total cholesterol (TC), triglyceride (TG), postprandial 2 h blood glucose (2 hPG), fasting blood glucose (FPG).)], serum thyroxine [high-sensitivity thyroid stimulating hormone (S-TSH), free triiodothyronine (FT3), free thyroxine (FT4), total triiodothyronine (TT3), total thyroxine (TT4)], Cystatin C (CysC) and beta 2-microglobulin (beta 2-MG) level changes of patients in two groups were compared. Results: The total effective rate of the observation group was 88.00% significantly higher than that of the control group (76.00%) (P<0.05). The levels of LDL-C, TC and TG of patients in the two groups were significantly higher than those before treatment, and the levels of 2hPG and FPG were significantly lower than those before treatment (P<0.05). The levels of LDL-C, TC and TG in the control group were significantly increased (P<0.05). After treatment, the levels of S-TSH in the two groups were significantly higher than those before treatment, and the levels of FT3, FT4, TT3 and TT4 were significantly lower than those before treatment (P<0.05). The levels of CysC and beta 2-MG in the two groups were significantly lower than those before treatment (P<0.05). The levels of CysC and beta 2-MG of patients in the observation group were significantly lower than those in the control group (P<0.05). There was no significant difference between the two groups with respect to the incidence rate of adverse reactions (P>0.05). Conclusion: Methimazole is effective in the treatment of hyperthyroidism, which can effectively improve serum thyroxine, beta 2-MG and CysC levels, and has little effect on glycolipid metabolism.