Objective To compare the differences in clinicopathological features, molecular phenotypes, and prognosis between atypical type A thymoma (AAT) and classic type A thymoma (TAT), and to clarify the aggressive nature of AAT. Methods The data of AAT patients (AAT group) and classic TAT patients (TAT group) who underwent surgical resection for thymoma at West China Hospital of Sichuan University between January 2016 and November 2024 were retrospectively collected. Comparisons on the clinical data, histopathology, immunohistochemistry (CD20, Ki67), GTF2I mutation status, and survival outcomes were performed between the two groups. Results A total of 53 patients were enrolled, including 22 in the AAT group and 31 in the TAT group. There was no significant difference in age, sex, or initial presenting symptoms between the two groups (P>0.05). Compared with the TAT group, the AAT group had larger tumors [(5.6±2.7) vs. (4.1±2.0) cm, P=0.043], a lower proportion of Masaoka stage Ⅰ (31.6% vs. 61.3%, P=0.041), and worse survival outcomes [progression-free survival: hazard ratio (HR)=0.046, 95% confidence interval (CI) (0.23, 0.89), P=0.004; overall survival: HR=0.36, 95%CI (0.19, 0.69), P=0.013]. Pathologically, the AAT group showed more mitotic figures (mean 6/2 mm2), and tumor necrosis was observed in 45.5% of cases. There was no statistically significant difference in the CD20 expression rate (20.0% vs. 41.9%), Ki67 index [(11.0±6.0)% vs. (8.0±6.9)%], or GTF2I mutation rate (86.7% vs. 92.3%) between the two groups (P>0.05). Conclusions AAT is a subtype of TAT with distinct aggressive pathological features, including higher mitotic activity, a tendency for necrosis, and a greater propensity for recurrence and metastasis. Pathological diagnosis should integrate morphology and molecular testing to guide more aggressive treatment and follow-up strategies.