Cell density has profound impacts on the cell culture practices of human pluripotent stem cells. The regulation of cell growth, cell death, pluripotency and differentiation converge at high density, but it is largely unknown how different regulatory mechanisms act at this stage. We use a chemically defined medium to systemically examine cellular activities and the impact of medium components in high-density culture. We show that medium acidosis is the main factor that alters cell cycle, gene expression and cellular metabolism at high cell density. The low medium pH leads to inhibition of glucose consumption, cell cycle arrest, and subsequent cell death. At high cell density, the suppression of medium acidosis with sodium bicarbonate (NaHCO3) significantly increases culture capacity for stem cell survival, derivation, maintenance and differentiation. Our study provides a simple and effective tool to improve stem cell maintenance and applications.