Diafiltration had been widely used in milk protein fractionation for almost thirty years to produce casein-enriched retentate. Among them, intermittent feed diafiltration was the only way ever used. But we noted some other diafiltration types had been used in other fields such as chemical engineering. In this study. The separation performance, chemical properties, component resistance and mass balance analysis were compared under different diafiltration types, aiming to find suitable diafiltration processes for milk protein fractionation. Research suggested that different diafiltration process may have different advantages. From the separation performance point of view, the highest removal rate of native whey proteins was observed under variable volume diafiltration (VVD) mode. But in terms of average flux, constant volume diafiltration (CVD) mode was utmost time and energy saving with an average flux of 81.25 kg m−2h−1. In addition, the percentage loss of protein under CVD and constant volume concentration ratio diafiltration (CVCRD) mode were significantly lower than that of other diafiltration modes (P < 0.05), indicating fewer protein were absorbed or compacted by the membrane. Therefore, diafiltration type should be selected according to the purpose of production.