Forkhead box Q1 (FOXQ1) is a nuclear transcription factor that controls the transcriptional activity of downstream genes to exert biological effects. Since its regulatory role in colorectal cancer (CRC) is unknown, we correlated RNA-seq and ATAC-seq sequencing data from the Cancer Genome Atlas Program (TCGA), the Gene Expression Omnibus (GEO), and other databases with FOXQ1 knockdown data from our group and normal DLD1-CRC cell lines. First, we analyzed FOXQ1 gene expression across multiple databases and datasets and found significant differences in FOXQ1 gene expression in most tumors. In addition, we performed an extension analysis of the FOXQ1 gene at different levels and found a close relationship between the FOXQ1 gene and immunity. Then, based on the FOXQ1 gene, we collected its target genes and obtained a total of 107 genes that met the regulatory trend. After a series of target gene analyses, we obtained three key genes (SERPINA1, MYL9, and CFTR). Moreover, an enrichment analysis, an independent prognostic analysis, and an immune-related analysis were performed around FOXQ1 and its target genes. After knocking down FOXQ1 protein in SW480 cells, the SERPINA1 and MYL9 proteins were significantly altered, though the CFTR protein was not significantly changed. These results provide bioinformatics data that support studying and exploring the FOXQ1 gene and its target genes in CRC.