Mycotoxins produced by different species of fungi may coexist in single cereal and feedstuff samples, which could become highly toxic for humans and animals. In order to quantify four mycotoxins (zearalenone, fumonisin B1, deoxynivalenol, and aflatoxin B1) in cereal and feedstuff samples simultaneously, a new suspension array immunoassay was developed. Antimycotoxin monoclonal antibodies were conjugated to the surface of different encoding microspheres (19#, 37#, 39#, and 49#), and mycotoxin-protein conjugates were then coupled with biotin. Using streptavidin-phycoerythrin as a signal reporter protein, this direct competition multiple suspension array immunoassay was optimized. The results showed that the detection limits for zearalenone, fumonisin B1, deoxynivalenol, and aflatoxin B1 were 0.51, 6.0, 4.3, and 0.56 ng/mL, respectively, with detection ranges of 0.73-6.8, 11.6-110.3, 8.6-108.1, and 1.1-14.1 ng/mL, respectively. For the detection of the spiked samples, the recovery rates were between 92.3% and 115.5%. This method also shows a good correlation coefficient (r = 0.99, P < 0.01) with liquid chromatography-tandem mass spectrometry in the detection of toxins in commercial cereal and feedstuff samples. This suspension array immunoassay was high-throughput and accurate for the rapid quantitative detection of multiple mycotoxins in commercial cereal and feedstuff samples.