Background <p>Colorectal cancer (CRC) is a prevalent malignant neoplasm characterized by high incidence and mortality rates. Currently, the role of microRNAs (miRNAs) in CRC is increasingly recognized. In this study, we aim to investigate the prognostic value of miR-363-5p and its associated molecular mechanisms.</p> Methods <p>A total of 156 paired samples were collected from patients with CRC. The levels of miR-363-5p in the samples were detected by RT-qPCR. KM curves and multivariable Cox regression models evaluated the prognostic value of miR-363-5p. Flow cytometry, CCK-8 assay and Transwell assay examined the effects of miR-363-5p on cellular malignant phenotypes. Dual-luciferase reporter assays validated the targeting relationship.</p> Results <p>The expression level of miR-363-5p was declined in CRC, and patients with TNM stage III + IV exhibited lower miR-363-5p expression compared to those with TNM stage I + II. Furthermore, individuals with low miR-363-5p expression demonstrated shorter overall survival than those with high expression, and miR-363-5p was confirmed as an independent protective factor for CRC. In vitro, miR-363-5p suppressed cellular malignant phenotypes, primarily manifested by miR-363-5p mimic promoting apoptosis while inhibiting proliferation, migration and invasion. Mechanistically, we identified MEIS3 as a direct target of miR-363-5p, and rescue experiments confirmed that MEIS3 overexpression attenuated the tumor-suppressive effects of miR-363-5p.</p> Conclusions <p>Downregulated miR-363-5p were involved in CRC progression and associated with poor patient prognosis. Mechanistically, upregulated miR-363-5p suppressed the malignant cellular phenotype by negatively regulating MEIS3, thereby inhibiting the progression of CRC.</p>