Ascl2, a downstream target of WNT signaling, controls the fate of colorectal cancer (CRC) progenitor cells. This study aims to explore the prognostic significance of transcription factor Ascl2 regulated acyl-CoA short chain fatty acid synthatase-1/3 expression in CRC patients.Methods GSE69036, GSE34926 and GSE44076 were downloaded from the GEO database. The mRNA expression levels and related clinical information of CRC patients were downloaded from TCGA database. The correlation between Ascl2 and Acss1/3 expression levels was analyzed by Spearman rank correlation analysis. Ascl2 and Acss1/3 mRNAs and miR-4282 were determined by real-time PCR, and Ascl2 and Acss1 proteins were assesses by Western blot in sh-Ascl2/LS174T and their control cells. The survival for CRC patients was analyzed by Kaplan-Meier analysis and Cox regression analysis.Results GSE69036, GSE34926 gave the evidence of 2. 08 fold downregulation of Acss1 and 2. 069 fold upregulation of miR-4282 in sh-Ascl2/LS174T cells which was confirmed by real-time PCR, and Western blot confirmed the decrease of Ascl2 and Acss1 protein levels in sh-Ascl2/LS174T cells. Ascl2 and Acss1 mRNA levels in the cancerous tissues from CRC patients were significantly higher than peri-cancerous tissues (P＜0.001), whereas Acss3 mRNA levels in the cancerous tissues were significantly lower than peri-cancerous tissues (P＜0.001). Ascl2 mRNA levels in the cancerous tissues was inversely correlated with Acss3 mRNA levels, and positively correlated with Acss1 mRNA levels (P＜0.001). Ascl2 and Acss3 mRNA levels were not related to the progression free survival (PFS), disease-specific survival (DSS) and overall survival (OS) of CRC patients, the DSS and OS in high Acss1 expression group were significantly lower than low Acss1 expression group (P=0.0389 and P=0.04). The combined abnormal expression of Ascl2 and Acss1, and combined abnormal expression of Ascl2, Acss1 and Acss3 were related to the DSS of CRC patients (P=0.037 and P=0.0161), the combined abnormal expression of Ascl2, Acss1 and Acss3 was one of the risk factors for DSS in CRC patients (P=0.043).Conclusion Ascl2 might regulate Acss1/3 expression in CRC cells and lead to the remodeling of short chain fatty acid β-oxidation. Their combined expression pattern in CRC tissues were related to CRC patient prognosis