We developed an ultrasensitive low-background chemiluminescence enzyme immunoassay (CLIA) for multiplex mycotoxin detection using silica-hydrogel photonic crystal microsphere (SHPCM) suspension arrays. The interspace of SHPCM was occupied by hydrogel material and retained the structure color of SPCM, which not only could encode microsphere carriers with their positions of reflection peaks or structure colors but reduce the non-specific protein adsorption and result in a low background signal. Comparison with SPCM and glass beads, SHPCM could provide the more wide dynamic detection linear range and lower background signal. The linear detection range was 0.0001–1ng/mL, 0.001–10ng/mL, and 0.0001–1ng/mL for AFB1, FB1 and OTA, respectively. The recovery rates in rice, corn and wheat samples for AFB1, FB1 and OTA were between 74.96±5.82%–104.87±5.77%. The positive results detected by this method in 20 real cereal samples were confirmed by high performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS). The results indicate that the SHPCM suspension array can be used to high throughput and sensitive screening for multiplex mycotoxins in cereal samples.