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Calcium (Ca) is an essential mineral nutrient and plays a crucial signaling role in all living organisms. Increasing Ca content in staple foods such as rice is vital for improving Ca nutrition of humans. Here we map a quantitative trait locus that controls Ca concentration in rice grains and identify the causal gene as GCSC1, which encodes a chloroplast vesicle localized homo-oligomeric protein. GCSC1 exhibits Ca 2+ transport activity and functions as a Ca 2+-permeable channel to mediate the efflux of Ca 2+ from the chloroplast to the cytosol. Knockout of GCSC1 results in increased chloroplast Ca concentration, lower stomatal conductance in leaves and enhanced Ca allocation to grains. Natural variation in grain Ca concentration is attributed to the variable expression of GCSC1 resulting from its promoter sequence variation. Our study identifies a new type of chloroplast Ca 2+-permeable channel that mediates chloroplast Ca 2+ efflux and provides a way to biofortify Ca in rice to benefit human nutrition.