Smoking cessation prolongs survival and decreases mortality of patients with non‐small‐cell lung cancer (
NSCLC
). In addition, epigenetic alterations of some genes are associated with survival. However, potential interactions between smoking cessation and epigenetics have not been assessed. Here, we conducted an epigenome‐wide interaction analysis between
DNA
methylation and smoking cessation on
NSCLC
survival. We used a two‐stage study design to identify
DNA
methylation–smoking cessation interactions that affect overall survival for early‐stage
NSCLC
. The discovery phase contained
NSCLC
patients from Harvard, Spain, Norway, and Sweden. A histology‐stratified Cox proportional hazards model adjusted for age, sex, clinical stage, and study center was used to test
DNA
methylation–smoking cessation interaction terms. Interactions with false discovery rate‐
q
≤
0.05 were further confirmed in a validation phase using The Cancer Genome Atlas database. Histology‐specific interactions were identified by stratification analysis in lung adenocarcinoma (
LUAD
) and lung squamous cell carcinoma (
LUSC
) patients. We identified one CpG probe (cg02268510
SIPA
1L3
) that significantly and exclusively modified the effect of smoking cessation on survival in
LUAD
patients [hazard ratio (
HR
)
interaction
= 1.12; 95% confidence interval (
CI
): 1.07–1.16;
P
=
4.30 × 10
–7
]. Further, the effect of smoking cessation on early‐stage
LUAD
survival varied across patients with different methylation levels of cg02268510
SIPA
1L3
. Smoking cessation only benefited
LUAD
patients with low methylation (
HR
= 0.53; 95%
CI
: 0.34–0.82;
P
=
4.61 × 10
–3
) rather than medium or high methylation (
HR
= 1.21; 95%
CI
: 0.86–1.70;
P
=
0.266) of cg02268510
SIPA
1L3
. Moreover, there was an antagonistic interaction between elevated methylation of cg02268510
SIPA
1L3
and smoking cessation (
HR
interaction
= 2.1835; 95%
CI
: 1.27–3.74;
P
=
4.46 × 10
−3
). In summary, smoking cessation benefited survival of
LUAD
patients with low methylation at cg02268510
SIPA
1L3
...