Non-small-cell lung cancer (NSCLC) is an important cause of cancer-related death worldwide. The distant metastasis heterogeneity of gene tumor mutations in tumors of NSCLC patients brings critical challenges for treatment. We sequenced the primary tumors and metastatic tissues of 48 NSCLC patients through 363 tumor-related gene panels to examine gene mutations in primary tumors and metastatic tissues, and screen candidate carcinogenic and metastatic-related driver mutations. The patient group included 21 patients in the metastatic group and 27 patients in the non-metastatic group. The patient's median age was 62 years and 54% (26/48) of patients were women. Approximately 75% (36/48) of patients were non-smokers. The mutation spectrum results showed that epidermal growth factor receptor (EGFR) gene mutation was the most frequent mutation (68.75%), followed by TP53 mutation (45.83%); 19del accounted for the largest proportion of EGFR mutations. Copy number variation (CNV) mutation spectrum results showed that EGFR amplification was more common in the metastatic group than the non-metastatic group. The mutant-allele tumor heterogeneity value of the metastatic group was higher than that of the non-metastatic group (p = 0.013). The progression-free survival of the metastatic group was significantly shorter than that in the non-metastatic group (p = 0.041). Single nucleotide variant difference analysis showed that the frequency of TP53 mutations was higher in the metastasis group. The number of subclonal mutations in the primary and metastatic lesions in the metastasis group was significantly different; the number of subclonal sites in metastatic lesions was higher than that in primary lesions. Our results suggested that the gene mutations of NSCLC in primary and metastatic lesions and identified specific mutations related to metastasis of NSCLC. Our research will help to clarify key differences between gene mutations between primary and metastatic NSCLC. These findings will help to provide new theoretical support for the future targeted therapy of metastatic NSCLC.