The aim of this study was to evaluate whether molecular classification was associated with treatment response in women with endometrial endometrioid carcinoma (EEC) or Endometrial atypical hyperplasia/endometrial intraepithelial neoplasia (EAH/EIN) treated with progestin. A retrospective analysis of 59 patients with EEC or EAH/EIN who received fertility-sparing therapy between 2013 and 2021 was performed. For each patient, medical records and pathological reports were reviewed. The treatment efficacy and tumor prognosis were evaluated. Immunohistochemistry analysis for p53 and MSH2, MSH6, PSM2, MLH1 were performed. Molecular classification was analyzed using a 11-gene panel based on next generation sequencing technology. 23 of 39 patients with EEC received complete response (CR) after fertility-sparing treatment which was significantly lower than the EAH/EIN group (58.97% vs 80.0%, P<0.05). Molecular classification via the Cancer Genome Atlas (TCGA) algorithm was successfully applied to 59 cases. The distribution of specimens into the four molecular classes was as follows: 83.05% (49/59) CNL(copy number-low),6.78% (4/59) MSI-H (microsatellite instability -high), 5.08%(3/59) POLE-mutated and 5.08% (3/59) CNH(copy number-high). MSI and TP53 sequencing results were concordant with immunohistochemistry analyses of MMR and p53 protein. The patients with CNH and MSI-H subtypes showed worse prognosis than those with POLE-mutated and CNL subtypes. Molecular classification of EAH/EIN prior to management with progestin treatment was feasible and may predict patients at risk of progression.