Mycotoxins, such as fumonisin B1 (FB1) and deoxynivalenol (DON), are toxic secondary metabolites produced by fungi. Herein, the simultaneous detection of FB1 and DON (both of which are water-soluble) in grain samples by immunochromatographic methods was used to probe whether the levels of these mycotoxins exceeded the limit of 1 mg/kg. Two types of immunochromatographic test strips (ICSs) were developed for this purpose, namely, those based on Au nanospheres (prepared via reduction with trisodium citrate) and Au nanoflowers (prepared by Au seed-mediated growth) as markers, with the respective sensitivities to both FB1 and DON equalling 20 and 5.0 ng/mL. The former ICS was used to detect FB1 and DON in grain (51 wheat samples and 18 maize samples), providing results consistent with those of high-performance liquid chromatography and enzyme-linked immunosorbent assays. The developed technique was suitable for the on-site screening of large-scale samples for FB1 and DON.