The extraction of zirconium (Zr) and hafnium (Hf) in methyl isobutyl ketone (MIBK)—thiocyanic acid (HSCN) system has been widely used in the production of nuclear-grade zirconium and hafnium in industry, while the extraction mechanism was not adequately studied. In this study, the extraction and stripping equilibrium of Zr and Hf in the MIBK-HSCN system was studied. The results showed that elevated HCl concentration can increase the distribution ratio of SCN− and decrease that of Zr/Hf in organic phase. In the stripping process, HCl concentration and the Organic/Aqueous (O/A) phase ratio played important roles. The mechanism of the extraction reaction was discussed by considering the stoichiometric relationship of possible reaction equations and corresponding equilibrium constants. The results indicated that SCN− could be extracted into MIBK as HSCN·MIBK. Meanwhile, SCN− could also be extracted into MIBK by complexing with metal (Zr or Hf). The molar ratios of MIBK to the complexes of Zr and Hf have been found to be 5.34 and 5.03, respectively. With the increase in the initial concentration of HCl in the aqueous phase, the complexation molar ratios of SCN− to Zr and Hf increased first and then decreased, and so do the extraction equilibrium constants, which might be due to the extraction competition of HSCN and metal complexes.