To investigate the effect and molecular mechanism of ezetimibe on colorectal cancer (CRC), our study found that ezetimibe significantly inhibited the proliferation and progression of CRC. Further study showed that RPS6KA2 might be the target gene of ezetimibe treatment on CRC. RPS6KA2 expression was significantly lower in human CRC tissue samples and associated with T classification and vascular invasion of tumor cells. RPS6KA2 inhibited proliferation, migration, and invasion of CRC cells. The underlying mechanisms indicated that interaction between RPS6KA2 and PCSK9 was observed within the cytoplasmic compartment of CRC cells. RPS6KA2 suppressed PCSK9 and MAPK signaling pathway in CRC cells. BI-D1780 which is an inhibitor of RPS6KA2 increased PCSK9 and MAPK signaling pathway related proteins expression in SW620 cells. However, an inhibitor or stimulator of MAPK did not affect RPS6KA2 and PCSK9 expression, respectively. In vivo, CRC cells with RPS6KA2 or PCSK9 overexpression could inhibit or promote tumor growth and metastasis, respectively. PCSK9 promoted proliferation, migration, and invasion of CRC cells. PCSK9 expression was higher in human CRC samples and associated with N classification and TNM stage of CRC. In conclusion, our study firstly suggests that ezetimibe suppresses CRC progression by upregulating RPS6KA2 while downregulating PCSK9/MAPK signaling pathway.