The decolorization process of maize germ oil can simultaneously reduce the contents of beneficial lipid accompaniments for enhancing human health and risk factors. Herein, the decolorization rate, oil qualities (acid and peroxide values), lipid accompaniments (tocopherols and sterols), and risk factors, such as 3-chloropropanol esters (3-MCPDEs), glycidyl esters (GEs), were used as indicators for optimizing the decolorization condition. Results showed that by under heating at 85 °C for 30 min with magnesium silicate and activated clay (1:2, w/w), the tocopherols and sterols contents were 688.07 mg/kg and 9.89 g/kg, respectively. The 3-MCPDEs and GEs contents were 1.177 and 0.090 mg/kg, respectively, which meet the standard requirements according to the EU limit regulations for 3-MCPDEs and GEs in 2021. These results could provide a theoretical basis for the corn oil refining process and technical improvement.