Context: One of the sensitive markers for autoimmune thyroid disease (AITD) clinical identification is TRAb. To quickly distinguish TRAb with distinct antigenic epitopes, a straightforward and uncomplicated technique has not yet been created. Objective: To search for molecular diagnostic targets for different types of AITD (Graves' disease (GD), Graves' orbitopathy (GO), GD with III degree goiter (GD(3)), Hypothyroidism combined with positive TRAb (HT(TRAb+))) as molecular diagnostic targets. Methods: Following action on thyroid cells, differential genes (DEGs) generated by TRAb with distinct antigenic epitopes were detected and identified by RNA-seq, bioinformatics analysis, and RT-qPCR in the serum of AITD patients. Using the EdU assay, the effect of co-culturing thyroid cells with different antigenic TRAb epitopes on the cells' capacity to proliferate was investigated. Results: Bioinformatics analysis and RT-qPCR validation identified one GD key gene (AHSG), two GO key genes (ADRA1D and H2BC18), two GD(3) key genes (SOCS1 and CYBB), and one HT (TRAb+) key gene (MASP2). Correlation analysis and ROC curves showed that the above genes could be used as molecular diagnostic targets for different types of AITD. Finally, EdU results showed that TRAb inhibited thyroid cell proliferation in the HT (TRAb+) group compared with the normal control group, while the remaining three groups promoted thyroid cell proliferation, with a statistically significant difference (P < 0.05). Conclusion: We identified six key genes for different types of AITD, which have diagnostic value for different types of AITD. Meanwhile, we found that TRAb of different antigenic epitopes in AITD have different biological functions.