The role of gut microbiome in colorectal cancer (CRC) lung metastases is still unclear. Herein, we collected primary colorectal tumors, matched lung metastasis, and adjacent normal colon from seven patients for 16S rRNA sequencing to evaluate microbiome signature in distant site metastasis and analyze prognosis. Fecal samples from 19 non-metastases CRC patients and 11 CRC lung metastases patients were analyzed for validation. Our efforts led to a discovery of comprehensive microbiome in CRC lung metastatic tumors, characterized by a decreased microbial diversity and an increase bacterial interaction between gram-negative bacteria Stenotrophomonas and Brevundimonas . The primary-metastatic tumor pairs harbored highly similar microbial composition in both genus and species level, especially the high level of Stenotrophomonas maltophilia . Correspondingly, the S. maltophilia levels were positively associated with poor prognosis and cancer progression. Our work highlights the great potential of S. maltophilia and its associated microbiome as biomarkers in pathogenesis and prognosis of CRC lung metastases.