Rapid and accurate immune monitoring plays a decisive role in effectively treating immune-related diseases especially at point-of-care, where an immediate decision on treatment is needed upon precise determination of the patient immune status. Derived from the emerging clinical demands, there is an urgent need for a cytokine immunoassay that offers unprecedented sensor performance with high sensitivity, throughput and multiplexing capability, as well as short turnaround time at low system complexity, manufacturability and scalability. In this paper, we developed a label-free, high throughput cytokine immunoassay based on a magnet patterned Fe3O4/Au core-shell nanoparticle (FACSNP) sensing array. By exploiting the unique superparamagnetic and plasmonic properties of the core-shell nanomaterials, we established a facile microarray patterning technique that allows the fabrication of uniform, self-assembled microarray in a large surface area with remarkable tunability and scalability. The sensing performance of the FACSNP microarray was validated by real-time detection of four cytokines in complex biological samples, showing high sensitivity (~ 20 pg/mL), selectivity and throughput with excellent statistical accuracy. The developed immunoassay was successfully applied for rapid determination of functional immunophenotype of leukemia tumor associated macrophages, manifesting its potential clinical applications for real-time immune monitoring, early cancer detection, and therapeutic drug stratification towards personalized medicine.