Objective To investigate the effect of different organ metastases on clinical prognosis in patients with small cell lung cancer (SCLC). Methods A total of 10 347 SCLC patients with distant metastases (M1) obtained from the surveillance, epidemiology, and end results (SEER) database between 2010 and 2013 were enrolled in this study. The median duration of follow-up was 4 months and the median age was 67 years. According to metastatic sites, the patients were divided into six groups:bone metastasis group, brain metastasis group, liver metastasis group, lung metastasis group, none group (no metastasis found in the bone, brain, liver or lung) and multi-organ metastasis (MOM) group (2 or more organ metastases found in the bone, brain, liver or lung). The effects of different organ metastases on clinical prognosis in SCLC patients were analyzed. Results MOM was the most common pathway of metastasis, accounting for 32.8% (3 396/10 347), followed by liver metastasis (19.0%, 1 971/10 347), brain metastasis (12.1%, 1 251/10 347) and bone metastasis (10.0%, 1 033/10 347). The mortality rates associated with bone, brain, liver and lung metastases and MOM were 77.2% (797/1 033), 74.1% (927/1 251), 82.4% (1 625/1 971), 73.4% (504/687), and 81.6% (2 770/3 396), respectively. Compared with the none group, the MOM and liver metastasis groups had higher hazard ratio (HR) (95% confidence interval[CI] of 1.80 (1.66-1.96) and 1.69 (1.54-1.85), respectively, followed by bone and brain metastasis groups with HR (95% CI) of 1.24 (1.12-1.39) and 1.28 (1.16-1.42) (all P<0.001). Lung metastasis group had a lowest HR (95% CI) of 1.07 (0.95-1.21) (P=0.27). Conclusion MOM and liver metastases are associated with the worst prognosis and the highest mortality in SCLC patients, followed by bone, brain and lung metastases. Therefore, for the SCLC patients with distant metastasis, different treatments should be carried out according to involved organs, and treatment should be strengthened in patients with liver metastasis and MOM.