This study investigated the content of deoxynivalenol (DON), sugars, proteins, phenolics, amino acids, the antioxidant capacity and antioxidant enzymes activities of Fusarium naturally contaminated wheat (FCW) during soaking and germination. Results showed that the concentration of DON in FCW was less than 100 mu g/kg after soaking and 4 days of germination. Total sugar and protein contents did not change, significantly. However, free amino acids content increased in wheat sprouts. Meanwhile, the content of reducing sugar decreased on day 1 of germination but increased thereafter. Bound phenolics content decreased by 82.57% after soaking. A significant increase of free phenolics content was found only on the third day of germination. The change of ABTS radical scavenging capacity was consistent with that of total phenolics content, and DPPH radical scavenging capacity increased constantly during germination. Interestingly, superoxide dismutase (SOD) activity decreased significantly in 1-day-germinated sprout. The activities of peroxidase (POD), ascorbate peroxidase (APX) and Catalase (CAT) enhanced by 1.18, 1.9 and 3.31 times, respectively, after 4-day germination. In conclusion, soaking had a negative impact on nutritional quality and phenolics content of Fusarium contaminated wheat and germination can enhance its antioxidant capacity by increasing phenolics content and regulating the activities of antioxidant enzymes.