Psychostimulants, such as amphetamine-type stimulants, induce alterations in hypothalamic-pituitary-thyroid (HPT) axis function. In this study, we sought to investigate the changes in the HPT axis using a well-characterized non-human primate model after chronic exposure to methamphetamine (MA). The data collected from 10 adult monkeys were retrospectively studied, assigning them into two groups-the control group (saline) and MA group. MA was injected for 4 weeks with gradually increasing dose, and later injected maintenance doses for 24 weeks. We collected and tested the blood samples on a weekly basis for T4, free T4, T3, free T3, TSH, TgAb, and TPOAb. We used western blotting and quantitative reverse transcription polymerase chain reaction techniques to test the protein and mRNA expression of bcl-2, Bax, and thyroid stimulating hormonereceptor. The MA group had significantly higher levels of T4, FT4, T3, and TSH than the control group. However, no significant difference was observed in FT3, TGAb, and TPOAb. Compared with the control group, most of the thyroid from the MA group consistently showed markedly disordered structure: varied size, lymphocytic infiltration, and local fibrosis. In the MA group, the protein and mRNA expression of Bax were significantly higher than the control group, whereas the protein and mRNA expression of Bcl-2 and TSH-R were significantly lower. These results indicate that chronic exposure to MA can lead to changes in the HPT axis function and induce apoptosis or other microdamage to the thyroid gland in a non-human primate model.