Objective To explore the consistency of circulating tumor DNA (ctDNA) in peripheral blood of patients with non-small cell lung cancer (NSCLC) with epithelial growth factor receptor (EGFR) and phosphatidylinositol 3-kinase catalytic subunit α (PIK3CA) gene mutations in pathological tissues, and analyze the influencing factors. Methods One hundred and eighteen patients with NSCLC treated in our hospital from December 2019 to December 2020 were selected as the subjects of the study. The gene status of EGFR, PIK3CA, c-Met, TP53, FGFR1, BRAF, STK11, FANCA, KRAS and ERBB2 in peripheral blood ctDNA and pathological tissue were detected, and the consistency of EGFR and PIK3CA in ctDNA and tissue was compared, and the patients were divided into consistent group and inconsistent group. The clinical data of the two groups were compared, and the factors affecting the consistency of the results were analyzed by multivariate Logistic regression analysis. Kaplan-Meier method was used to draw survival curve to analyze the one-year survival of patients with EGFR and PIK3CA mutations detected by ctDNA. Results The results of ctDNA detection showed that at least one EGFR mutation was detected in 84 patients (71.19%). The detection rates of 19del, L858R and T790M were 37.29%, 23.73% and 33.05%, respectively. 33 cases (27.97%) detected at least one PIK3CA mutation, and the detection rates of p.E545K, p.H1047R and p.E542K were 15.25%, 9.32% and 4.24%, respectively. The results of tissue detection showed that the detection rate of EGFR mutation was 65.25%, and that of 19del, L858R and T790M was 35.59%, 23.73% and 31.36%, respectively, and that of p.E545K, p.H1047R and p.E542K was 12.71%, 7.63% and 3.39%, respectively. The mutation detection rates of c-Met, TP53, FGFR1, BRAF, STK11, FANCA, KRAS and ERBB2 in ctDNA were 1.69%, 22.03%, 2.54%, 4.24%, 5.08%, 3.39%, 1.69% and 1.69%, respectively, and 5.93%, 33.05%, 2.54%, 2.54%, 5.08%, 3.39%, 2.54% and 3.39% in tissues, respectively. The coincidence rates of ctDNA and tissue detection of EGFR, PIK3CA and population were 77.12%, 71.19% and 64.41%, respectively (Kappa=0.348, 0.537, 0.645). The results of multivariate analysis showed that poor differentiation, tumor stage Ⅳ, bone metastasis and initial diagnosis were independent risk factors for the consistency of EGFR and PIK3CA gene mutations in peripheral blood ctDNA and tissues (P<0.05). The survival rate of EGFR mutation positive patients was significantly lower than that of PIK3CA mutation negative patients, and the survival rate of PIK3CA mutation positive patients was significantly lower than that of PIK3CA mutation negative patients (P<0.05). Conclusion The consistency of PIK3CA detected by peripheral blood ctDNA and tissue DNA is good, but the consistency of EGFR is poor. The degree of tumor differentiation, stage, bone metastasis and initial diagnosis and treatment are all related to the consistency of detection