Purpose: In early-stage, Epidermal growth factor receptor mutation-positive (EGFR-M+) NSCLC, surgery remains the primary treatment, without personalized treatments. We aimed to identify risk factors for recurrence-free survival (RFS) to suggest personalized strategies. Patients and Methods: From January 2008 to August 2020, a total of 1,181 patients with pathological stage (pStage) IB–IIIA, non-squamous NSCLC. To identify clinicopathological risk factors, 1,181 patients with pStage IB–IIIA, common EGFR-M+ NSCLC were analyzed. Comprehensive genomic analysis was conducted in 56 matched case-control cases. Results: Among 1,181 patients, pStage IB, II, and IIIA comprised 48.9%, 28.0%, and 23.1% of subjects, respectively. Median RFS was 73.5 months, 48.7 months, and 22.7 months for each stage, respectively (P < 0.001). In multivariate analysis, pStage, micropapillary subtype, vascular invasion, pleural invasion, and pathological classification by cell of origin were associated with RFS. The non- terminal respiratory unit (non-TRU) of the RNA subtype (HR 3.49, 95%CI 1.72–7.09, P < 0.01) and TP53 mutation (HR 2.50, 95% CI 1.24–5.04, P = 0.01) were associated with poor RFS independent of pStage II or IIIA. After recurrence, patients with APOBEC mutation signature had inferior PFS of EGFR-TKI compared with that of patients without this signature (8.6 vs.·28.8 months, HR 4.16, 95%CI 1.28–13.46, P = 0.02). Conclusions: The low-risk group with TRU subtype and TP53 wild type without clinicopathological risk factors might not need adjuvant EGFR-TKIs. In the high-risk group with non-TRU subtype and/or TP 53 mutation, or clinicopathological risk factors, a novel adjuvant strategy including EGFR TKI and others needs to be investigated.