The coexistence of multiple mycotoxins poses a significant risk to the safety of agricultural products. Hence, a novel and automated magnetic beads-based chemiluminescence immunoassay (MCLIA) system was developed for the simultaneous quantification of typical multi-mycotoxins, including zearalenone (ZEN), Ochratoxin A (OTA), deoxynivalenol (DON), and aflatoxin B1 (AFB1). It comprises a compact chemiluminescence-based analyzer and a specially designed mycotoxin assay kit. Firstly, antimycotoxin monoclonal antibody (mAb) was coupled with alkaline phosphatase (AP), and the antigen of mycotoxin was then with biotin. After detailed optimization of this indirect competition immunoassay, all necessary reagents were preloaded and sealed into a specialized plastic reagent strip to prepare the assay kit. Secondly, a compact chemiluminescence-based analyzer was developed by programmatically integrating magnetic, thermal, and optical mechanisms. The MCLIA system facilitates the detection of mycotoxins in up to 8 samples simultaneously or various mycotoxins in different samples within 20 min, according to actual needs. The detection limits (LOD) for ZEN, OTA, DON, and AFB1 were 2.55, 0.64, 15.47, and 0.78 μg/kg, respectively, with the 50 % inhibition concentrations (IC50) in the ranges of 1.84−4.25, 0.95−1.69, 11.36−13.98, and 0.37−0.54 ng/mL. Parallel analysis of commercial agricultural products demonstrated a strong linear correlation (R2 = 0.9843–0.9962) with UPLC-HRMS, confirming the MCLIA system's reliability for the simultaneous quantitative detection of various mycotoxins. Offering advantages in detection sensitivity, dynamic range, and turnaround time, the compact MCLIA system facilitates automated and parallelized detection in the model of “sample-in to result-out”. It presents a versatile platform for the efficient immunodetection of other contaminants.