A suspension array with microcarriers encoded by both structural color and shape was developed. The microcarriers with high stability, large capacity, low background noise and simplicity for practical application were the hydrogel colloidal crystals fabricated by photolithography. The aptamer based multiplex array, as an example, was constructed using the encoded microcarriers as the carrier of suspension array. The ssDNA functionalized hydrogel microcarriers are achieved by co-polymerization. Based on the high selectivity recognition of aptamer to its target, a novel hydrogel microcarrier suspension array platform, as a potential tool for the efficient quantification of biomolecules, is established.