Understanding the complex regulatory network that determines stem cell fates requires a high-throughput platform that can generate a large number of precisely controlled microenvironments representing multiple factors for stem cell culture and analysis.Here we developed a superhydrophobic microwell array chip on which the culturing condition in each microwell can be spontaneously isolated by a grafted layer of superhydrophobic polymers.Simple steps for media exchange were developed to facilitate the on-chip culturing of both adherent and non-adherent cells for up to six days without compromising cell viability and functionality.The culture condition in each microwell was facilely manipulated using a robotic spotter.Stem cell niches combining soluble factors,extracellular matrix,and microtopographic cues were generated on a single 512-well SMARchip and their combinatorial effects on the fate of mouse Oct4-EGFP iPSCs were systematically probed.We observed significant differences in iPSC pluripotency and proliferation between adherent flat and suspended spherical cultures on our platform,which might provide insight to improve the stem cell technologies.