Background: Few patients with pulmonary sclerosing pneumocytoma (PSP) may suffer from recurrence and oligometastasis as it is a benign tumor or has a low malignancy potential. Herein, an in-depth study, based on an extremely rare PSP case with atypical features, was carried out to elaborate the potential mechanism underlying the rapid malignant progression. Methods: The clinicopathological data of this atypical PSP (AP) case were obtained. Formalin‑fixed and paraffin‑embedded tissues from all the lesions of AP and five classic PSP cases (as control) were used for whole-exome sequencing (WES) and immunohistochemistry. Results: A 23-year-old male showed a 6.5-cm pulmonary nodule in the right middle lobe (RML) and enlarged mediastinal lymph nodes (LNs). He underwent thoracoscopic RML lobectomy, systematic LNs dissection, and mediastinal lymphadenectomy. The metastases to the cervical LNs and liver were detected in a short period and then resected. Postoperative pathological examination confirmed the diagnosis of PSP in all the lesions, based on the typical histological characteristics and immunophenotypes. Furthermore, WES identified both AKT1 E17K somatic mutation and TP53 C176Y germline mutation in this AP case. The genomic evolution analysis showed different evolutionary branches in the metastatic tumors distinct from the primary lesion. Moreover, compared to the control group, the AP case showed high copy number variations (CNVs) and significantly high copy number instability (CNI). Conclusions: We speculated that the atypical histopathological features and malignant behaviors may be due to the co-mutations of somatic AKT1 E17K and germline TP53 C176Y, combined with the high CNVs and CNI.