Hashimoto’s thyroiditis (HT) and Graves’ disease (GD) are two very common autoimmune thyroid diseases (AITD). In this review, we use “HT in the hyperthyroidism stage” to refer to early HT with clinical manifestations of hyperthyroidism. In clinical practice, it is not easy to distinguish between HT in the hyperthyroidism stage and GD as they exhibit very similar clinical symptoms. The current literature lacks so far studies that systematically compare and summarize hyperthyroidism due to HT and GD from varied aspects. It is necessary to focus on all the clinical indices of HT in the hyperthyroidism stage and GD, for accurate diagnosis. Multiple databases such as PubMed, CNKI, WF Data, and CQVIP Data were used to search the literature concerning HT in the hyperthyroidism stage and GD. The information extracted from the relevant literature was summarized and further analyzed. To differentially diagnose hyperthyroidism as HT or GD, it is recommended to first focus on serological tests, followed by imaging tests, as well as the thyroid I131 uptake index. In pathology, fine needle aspiration cytology (FNAC) is the gold standard for the differential diagnosis of HT and GD. Test results from cellular immunology and genetics could also be used to accurately diagnose between the two diseases, which may be further developed and studied in the future. In this paper, we reviewed and summarized the difference between HT in the hyperthyroidism stage and GD from the following six aspects: blood tests, imaging, thyroid I131 uptake, pathology, cellular immunology, and genetics.