Multiple mycotoxins can contaminate foods simultaneously leading to increased risks for human health. To assess exposure and health risks of 9 mycotoxins, we employed a multiple immunoaffinity column – high performance liquid chromatography method to determine their concentrations of 35 whole wheat flour and 50 refined wheat flour samples from China. The recoveries of the validated method were 75.78–118.24%, and the limits of detection and quantification were 1.5–20 and 5.0–60 µg kg⁻¹, respectively. Multiple mycotoxins were detected in 37.1% of whole wheat flour and 8% of refined wheat flour. In the worst-case scenario, the hazard index was 222.69% for male and 253.97% for female with a cumulative exposure to Fusarium mycotoxins through consuming whole wheat flour, and deoxynivalenol was the main mycotoxin detected. In conclusion, whole wheat flour should be regarded with more health concern because of cumulative effects of co-occurred mycotoxins.