Epithelial to mesenchymal transition (EMT) is known to play a critical role in tumor metastasis, and this is an obstacle for hepatocellular carcinoma (HCC) treatment. Here, we found that NCAPG, a non-SMC subunit in the concentrate I complex, was upregulated in tumor tissues in HCC patients and was correlated with a poor prognosis. We also found that NCAPG could promote EMT though restraining the ubiquitination of β-catenin in HCC in vitro and in vivo. Through Immunoprecipitation-mass spectrometry (IP-MS) and Co-immunoprecipitation (Co-IP) assays, we found that NCAPG might interact with SIP, which is the central component in the E3 ubiquitin ligase composed by Siah1-SIP-Skp1-Ebi. Mechanistically, NCAPG could weaken the stability of this E3 ubiquitin ligase though competitive binding with SIP，and this was the important factor for ubiquitination of β-catenin suppression. When NCAPG was upregulated, the stability of this E3 ubiquitin ligase declined because the interactions between Siah1/SIP and SIP/Skp1 were weakened. The opposite phenomenon occurred when NCAPG was downregulated. Furthermore, we discovered that the disordered domain of NCAPG (D-NCAPG) serves as the specific binding sites for SIP binding. In conclusion, this study reveals the underlying mechanism by which NCAPG promotes EMT in HCC, which may be useful in the treatment of NCAPG-expressing HCC.