A 2-step fermentation process was developed to enhance antioxidant activity of monascal waxy corn, fermented by Monascus purpureus TISTR 3090, compared with the conventional method. The results showed that, after 8 days of fermentation, monacolin K content and pigment intensity of monascal waxy corn from 2-step fermentation were 62.89 mg kg−1 dry weight and 3072.70 unit g−1 dry weight, respectively, higher than those of the conventional method, while the residual reducing sugars were exhausted, giving the observed highest growth. The IC50 values of DPPH, ferric reducing/antioxidant powder (FRAP) and chelating ability on Fe2+ assays of the 2-step fermentation were about 50% less than those of the conventional method. A significantly positive correlation was found between pigment intensity and monacolin K content, while significantly negative correlations were found among monacolin K content, IC50 of FRAP and chelating ability on Fe2+. An ideal negative correlation between pigment intensity and chelating ability on Fe2+ was found.