Previous studies have shown that hyperthyroidism is associated with heightened insulin resistance and dyslipidemia. Therefore, in this study, we aim to explore the relationship between elevated thyroid hormone levels and the lipid profile in insulin resistance in patients with type 2 diabetes mellitus (T2DM) with hyperthyroidism. A total of 177 participants were included and grouped according to diagnosis. The serum test results demonstrated that free thyroxine (FT4) increased the insulin resistance index (HOMA-IR) by positively correlating with triglyceride (TG) levels (p = 0.005, r2 = 0.35). In patients with T2DM with hyperthyroidism, the decreasing high-density lipoprotein levels showed an association with HOMA-IR (p = 0.005). Among all the patients, with different levels of FT4, the areas under the ROC curve (AUCs) of the TG level, TG/high-density lipoprotein ratio, and HOMA-IR were 0.620 (95% CI: 0.536 to 0.698), 0.614 (95% CI: 0.530 to 0.692), and 0.722 (95% CI: 0.645 to 0.791), respectively. Our results suggest that elevated FT4 levels due to hyperthyroidism could alter the association with the lipid profile and insulin resistance in patients with T2DM. We also suggest that among all the included patients with T2DM, irrespective of the presence of hyperthyroidism, FT4 levels are positively correlated with insulin resistance.