Colorectal cancer (CRC) is one of the major causes of cancer-related mortality worldwide. Recent studies revealed that there is a relationship between CRC occurrence and microRNA (miRNA) function. Stem cells are a type of cells that have the ability to self-renew and to proliferate extensively while maintaining the undifferentiated state. Cancer stem cells (CSCs) are closely linked to tumor recurrence and metastasis. To this end, we evaluated the miRNA expression differences between colon CSCs and non-stem cells using the SW1116 cell line, to determine the relationship between tumor stem cells and tumor biological behavior. We isolated populations of colon CSCs with the CD133+/CD44+ and CD133-/CD44- surface phenotype from a human SW1116 colon adenocarcinoma cell line using flow cytometry. The expression of miRNA and mRNA of both sets of cells was examined with miRNA and mRNA arrays. Bioinformatic methods were used to analyze microarray results. We completed gene ontology analysis, pathway analysis, miRNA target gene prediction with databases. We identified a colon stem cell miRNA expression profile comprising 31 upregulated and 31 downregulated miRNAs, such as miR29a, miR29b, miR449b and miR4524. Some of these differentially expressed miRNAs may be involved in the regulation of stem cell differentiation. Gene ontology and pathway analyses showed that the differences are closely related to the function of the cell cycle, cell differentiation, signaling pathway, cytoskeletal proteins and cell-matrix adhesion in colon cancer stem cells. We found that miRNAs play an important role in regulating the expression of colon CSC characteristics. By regulating the expression of CSC signaling pathways, cytoskeleton and membrane proteins, miRNAs give tumor stem cells the macrobiological behavior of recurrence and metastasis. This study provides a new perspective on CRC metastasis and recurrence.