Abnormal climate changes have resulted in over-precipitation in many regions. The occurrence and contamination levels of mycotoxins in crops and cereals have been elevated largely. From 2017 to 2019, we did investigation targeting 15 mycotoxins shown in the wheat samples collected from Shandong, a region suffering over-precipitation in China. We found that deoxynivalenol (DON) was the dominant mycotoxin contaminating wheats, with detection rates 304/340 in 2017 (89.41%), 303/330 in 2018 (91.82%), and 303/340 in 2019 (89.12%). The ranges of DON levels were <4 to 580 mu g/kg in 2017, <4 to 3070 mu g/kg in 2018, and <4 to 1540 mu g/kg in 2019. The exposure levels were highly correlated with local precipitation. Male exposure levels were generally higher than female's, with significant difference found in 2017 (1.89-fold, p = 0.023). Rural exposure levels were higher than that of cities but not statistically significant (1.41-fold, p = 0.13). Estimated daily intake (EDI) and margin of exposure (MoE) approaches revealed that 8 prefecture cities have probabilistically extra adverse health effects (vomiting or diarrhea) cases > 100 patients in 100,000 residents attributable to DON exposure. As a prominent wheat-growing area, Dezhou city reached similar to 300/100,000 extra cases while being considered as a major regional contributor to DON contamination. Our study suggests that more effort should be given to the prevention and control of DON contamination in major wheat-growing areas, particularly during heavy precipitation year. The mechanistic association between DON and chronic intestinal disorder/diseases should be further investigated.