With high fat and protein content, maize germ is easily infected with fungus and mycotoxins during its storage. The qualities and safety of germ and its processing products may be affected by the storage. However, studies on the effect of storage on quality and polluted mycotoxin level of maize germ are limited. In this study, maize germ was stored with different initial moisture contents (5.03, 9.07, 11.82 and 17.97%) or at different relative humidity (75, 85 and 95%) for 30 days. The quality indices of germ (moisture content and crude fat content) and their produced germ oils (color, acid value and peroxide value) as well as the zearalenone (ZEN) and deoxynivalenol (DON) levels of germ, oils and meals were analyzed. Results showed that maize germ with high initial moisture contents (11.82, 17.97%) or kept at high humidity (95%) became badly moldy at the end of storage. Meanwhile, the qualities of these germ and oils showed great changes. However, the ZEN and DON contents of this maize germ, oils and meals stayed at similar levels (p < 0.05). Therefore, the storage could produce influence on the qualities of germ and oils, but showed limited effect on the DON and ZEN levels of germ and their processing products. According to this study, the storage condition of germ with no more than 9% moisture content and no higher than 75% humidity was recommended. This study would be benefit for the control of germ qualities and safety during its storage.