With the increasing demand for target biomarkers in multiplexed simultaneous detection, encoding technologies with sufficient encoding capacity are urgently needed. Here, we present a suspension array based on thickness-encoded, MIP-functionalized quartz microchip arrays for reaction and high-throughput detection. This platform incorporates a custom thickness-fluorescence decoding system that achieves micrometer-scale resolution over a millimeter dynamic range, allowing for 440 distinct codes. The platform demonstrates detection limits of 7.6, 7.9, and 15 mug mL(-1) for human, mouse, and rabbit IgG, respectively. Fabricated via a simple one-pot process, these arrays eliminate the need for expensive reagents or lithography, enabling high-throughput analysis. Quantitative multiplexed assays demonstrate high sensitivity, selectivity, and temporal stability, establishing this MIP-based platform as a robust tool for environmental monitoring, food safety, and clinical diagnostics.