The aim of this study was to explore the effect of different organ metastasis on the prognosis of non-small cell lung cancer (NSCLC). Patients with distant metastatic NSCLC were selected from Surveillance, Epidemiology, and End Results database during 2016 to 2019. The incidence of different organ metastasis and their association with clinicopathological factors were explored. Overall survival (OS) and lung cancer-specific survival (LCSS) for metastatic NSCLC were calculated, and multivariate Cox regression analysis was performed with a nomogram for OS being constructed based on Cox regression. Total 26,210 patients with distant metastatic NSCLC were included in this study. Around 48.9% of the metastatic NSCLC were multiple-organ metastasis and bone was the most commonly involved organ (44.4%). For patients with single-organ metastasis, the prognosis for lung or distant lymph nodes (LNs) metastasis was better than others (with median OS of 15 and 16 months for lung and distant LNs metastasis, respectively), and liver metastasis resulted in the worst prognosis with median OS of 8 months. A nomogram was constructed to visualize Cox regression model, along with the receiver operating characteristic (ROC) curve demonstrated good discrimination for the predictive model with 1- and 2-year area under the curve of ROC of 0.687 and 0.702, respectively. The prognosis of NSCLC patients with distant metastasis was poor. Liver metastasis results in the worst prognosis among the single-organ metastasis. The nomogram developed based on the Cox regression model has provided a useful tool to estimate the probability of OS of the metastatic NSCLC.