Abstract Objective The aim of this study was to investigate the role of serum IgE levels in the clinical features and outcomes of IgG4-related disease (IgG4-RD). Methods We retrospectively enrolled 459 newly diagnosed IgG4-RD patients with serum IgE examined at baseline from 2012 to 2019 and compared the clinical features between group A (serum IgE level ≤ 60 KU/L) and group B (serum IgE level > 60 KU/L). Subsequently, 312 patients who had been followed up for ≥ 1 year were further selected to evaluate the correlation between serum IgE level and disease outcome. Results At baseline, the serum IgE level was positively correlated with the serum IgG4 level (r = 0.1779, P = 0.0001), eosinophil count (r = 0.3004, P < 0.0001), and serum IgG level (r = 0.2189, P < 0.0001) in IgG4-RD patients. Compared with group A, group B had more patients with allergic diseases (P = 0.004), more organ involvement (P = 0.003), and higher IgG4-RD responder index scores (P = 0.002). During follow-up, group A patients had a higher remission induction rate than group B patients (88.4% vs. 73.6%, P = 0.035), while group B patients had a higher relapse rate than group A patients (29.0% vs. 16.2%, P = 0.039). Multivariate analysis found that a serum IgE level > 125 KU/L at baseline was a risk factor for disease relapse (hazard ratio [HR], 1.894 [95% confidence interval (CI) 1.022–3.508]; P = 0.042). Cox regression analysis showed that elevation of the eosinophil count was a risk factor for relapse in both group A and group B patients (HR, 8.504 [95% CI 1.071–42.511]; P = 0.009; and HR, 2.078 [95% CI 1.277–3.380]; P = 0.003, respectively), and the involvement of the lacrimal gland (HR, 1.756 [95% CI 1.108–2.782]; P = 0.017), submandibular gland (HR, 1.654 [95% CI 1.037–2.639]; P = 0.035), and kidney (HR, 3.413 [95% CI 1.076–10.831]; P = 0.037) were also risk factors for relapse in group B patients. Conclusion IgG4-RD patients with high serum IgE levels at baseline were more likely to have higher disease activity, and baseline high IgE levels were associated with disease relapse.