This study presents a new multiplex lateral flow immunoassay (LFIA) for the detection of aflatoxin B1 (AFB1), deoxynivalenol (DON), and zearalenone (ZEN). The multi-LFIA utilized phycocyanin (PC), a protein with excellent photophysical properties, as a fluorescent indicator for quantifying the three mycotoxins on a lateral flow strip platform. PC and monoclonal antibodies (mAbs) against AFB1, DON, and ZEN were immobilized onto carboxylated latex nanospheres (LNS) through a one-step coupling process. The resulting conjugates with strong red fluorescence were then used for multiplex sensing of AFB1, DON, and ZEN in wheat, corn, and animal feed. The visual results of the assay were obtained using LED UV lights coupled with a smartphone in less than 25 min. Under the optimal conditions, the new multi-LFIA achieved minimum detection limits of 1.04, 1.6, and 2.08 ng/mL for AFB1, 2.2, 6.45, and 2.9 ng/mL for DON, and 1.74, 1.67, and 2.11 ng/mL for ZEN in wheat, corn, and feed, respectively. The proposed method demonstrated high selectivity for AFB1, DON, and ZEN and showed strong correlation with LC-MS/MS results in spiked samples. In summary, the proposed method is feasible, rapid, and could serve as a highly sensitive platform for detecting AFB1, DON, and ZEN and other analytes in a single format.