Brain metastases explain the majority of lung cancer associated mortality, which is the leading cause of cancer death. Cytological analysis in the cerebrospinal fluid (CSF) remains the diagnostic gold standard, and the circulating tumor cells (CTCs) in CSF is not well defined at molecular and transcriptome level. We established an effective CSF-CTC collection procedure and isolated individual CSF cells from lung adenocarcinoma leptomeningeal metastases (LUAD-LM) patients and controls. 3,744 single-cell transcriptomes were sequenced and analyzed to perform a comprehensive characterization of CSF cells. Through clustering and expression analysis, we defined CSF-CTCs at the transcriptome level based on epithelial markers, proliferative markers and genes with lung origin. 290 genes are upregulated by 2-fold in LUAD-LM patients. These metastatic-CTC signature genes are enriched for metabolic pathway and cell-adhesion molecule categories, indicating their roles in tumor cell survival and metastases. We discovered substantial heterogeneity in patient CSF-CTCs, in sharp contrast to the lack of heterogeneity in cancer cell lines or xenograft models. We quantified the degree of heterogeneity and found significantly greater among-patient heterogeneity compared to among-cell heterogeneity within-patient. This observation could be explained by spacial heterogeneity of metastatic sites, cell-cycle gene expression profiles as well as the proportion of CTCs displaying mesenchymal and cancer stem-cell properties. In addition, our CSF-CTC transcriptome profiling allowed us to determine the biomarkers during the progression of an LM patient with cancer of unknown primary site (CUP). Our results will shed light on the mechanism of LUAD-LM and provide new directions of diagnostics and therapeutics of LM.