Effects of storage treatments on anthocyanin, fumonisin B1, aflatoxin B1 content of anthocyanin extract from purple corn were evaluated based on the harvest of 2008 and 2009 in north China. The anthocyanin content of anthocyanin extract from husk was 62.4 g/kg, being significant higher than that from cob and seed. The fumonisin B1 and aflatoxin B1 content of anthocyanin extract from the husk were 4.25 and 5.60 μg/kg, respectively, according with legislative limitation of USFDA. Moreover, the fumonisin B1 and aflatoxin B1 content of anthocyanin extract from the husk were lower than the maximum limitation of USFDA after each storage treatments. Therefore, the husk of the purple corn in north China was feasible for anthocyanin production due to its high anthocyanin content and low fumonisin B1 and aflatoxin B1 content.