Abstract Introduction Lung cancer is a leading cause of death from cancer worldwide, especially non-small cell lung cancer (NSCLC). The marker of progression in lung adenocarcinoma has been rarely studied. PD-1 is an effective drug target for the treatment of non-small cell lung cancer. The study of the effect of polymorphism on the progression of lung adenocarcinoma in the Han population of Northeast China may provide a valuable reference for the research and application of these drugs. Methods Chi-square test, Wilcoxon rank sum test, and classification efficacy assessment were used to teste SNPs of PD-1 in 287 patients and combined with clinical information. Results We successfully identified biomarkers (rs2227981, rs2227982, and rs3608432) that could distinguish the early stages and late stages of lung adenocarcinoma. Multiple clinical indicators showed significant differences among different SNP typing and cancer stages. Furthermore, this gene was confirmed to effectively distinguish the staging of lung adenocarcinoma with RNA-seq data in TCGA. Conclusions This indicated that the PD-1 gene and the SNPs on it could be used as markers for distinguishing lung adenocarcinoma staging in the Northeast Han population.