Objective The neutrophil to lymphocyte ratio (NLR) and platelet to lymphocyte ratio (PLR) have been identified as the biomarkers to predict systemic inflammation. However, there is less study to investigate the association between the biomarkers and thyrotoxicosis. Methods A total of 1 012 healthy subjects and 1 599 newly diagnosed thyrotoxicosis patients were enrolled in this study, including 978 in Graves′ disease (GD group), 452 in Hashimoto′s thyroiditis (HT group), and 169 in subacute thyroiditis (SAT group) groups. The clinical characteristics were retrospectively extracted from the medical records. The NLR and PLR at the baseline were calculated, the correlations between the NLR, PLR, and the clinical characteristics were analyzed. Results The NLR and PLR in SAT patients were significantly higher than those in the control, GD, and HT groups (all P<0.01), but were similar among the last three groups. The NLRs were positively correlated with white blood cell counts (r=0.5, P<0.01) and erythrocyte sedimentation rates (r=0.4, P<0.01), while the PLR was positively correlated with FT4 (r=0.16, P<0.05) and erythrocyte sedimentation rate (r=0.47, P<0.01). The SAT patients with abnormal liver function showed higher NLR and PLR compared the patients with normal liver function (all P<0.01). Based on the receiver operating characteristic curve, when to predict SAT patient with autoimmune thyrotoxicosis, the best cutoff value of NLR was 2.0 (sensitivity 80.5%, specificity 76.9%, area under curve 0.833), and the best cutoff value of PLR was 150 (sensitivity 64.3%, specificity 84.2%, area under curve 0.801). Conclusions The NLR and PLR values exhibited a dignostic value in the differentiation of SAT from autoimmune thyrotoxicosis.