A micropillar/microwell chip platform was applied to develop a 3D cell-based high-content screening (HCS) platform. Previously, 3D cell culture in the micropillar/microwell chip platform was only limited to cell viability measurements in a high-throughput manner. However, an HCS system could provide biological and phenotypic information which was very useful to understand complex biological functions and mechanisms of drug actions. To stain 3D cultured cells immobilized with alginate spots, we developed and optimized antibody staining procedures for 3D cultured cells. As a proof of concept, the phospho-EGFR (p-EGFR, a highly expressed receptor protein in cancer), F-actin (a protein of the actin cytoskeleton), and nuclei of 3D cultured cells were stained and analyzed after being treated with 72 different drugs. The p-EGFR inhibition of the drugs was successfully identified in the 3D cultured cells by comparing p-EGFR expression with that of F-actin and the nucleus. The p-EGFR expression levels were also measured by Western blot to verify the chip data.