Immunochromatographic assay (ICA) is a promising technology for on-site detection. Nonetheless, the wide-scale application of ICA is hindered by several disadvantages, such as poor reproducibility, low sensitivity, and single-target detection. Thus, a novel quantum dot nanobead (QB)-based multiplexed ICA (QB-ICA) with multiple test lines was developed in this study for the simultaneous quantitative detection of aflatoxin B (AFB) and zearalenone (ZEN), where QBs with high luminescence were used as labels to enhance the analytical sensitivity of the ICA. Moreover, a streptavidin (SA)-biotin system, which was undisturbed by the target mycotoxins, was introduced as the signal output for the control line. Consequently, stable and reliable T/C values (ratios of signals on the test line to that of the control line) were obtained as quantitative signals. The proposed QB-ICA demonstrated high sensitivity for the simultaneous detection of AFB and ZEN, of which the half-maximal inhibitory concentrations reached as low as 38.98 pg mL and 1.23 ng mL, respectively. At 10% competitive inhibition concentration, the limit detections (LOD) were 1.65 and 59.15 pg mL for AFB and ZEN, respectively. The average recoveries of the intra- and inter-assays ranged from 81.77% to 119.70% and from 94.18% to 111.4% for AFB and ZEN quantification, respectively, and the variation coefficients were less than 12%, thereby indicating that the proposed method is highly accurate and robust. These findings suggest that QB-ICA using SA-biotin system as the signal output of control line is an excellent point-of-care platform for the rapid screening of mycotoxins.