Nuclear Ca2+ regulates many signaling pathways including NFAT, CREB, MEF that are essential to cell immunity, development and differentiation. In current stage, there is no specified biochemical drugs to regulate nuclear Ca2+ individually. The existence of nuclear Ca2+ store remains unknown. In this study, we show the femtosecond-laser stimulation can precisely regulate nuclear and other subcellular Ca2+ stores exclusively. The stimulated Ca2+ store can be released but other subcellular Ca2+ stores are not interfered by femtosecond laser. By using this method, we present the evidence of the endogenous Ca2+ store inside nucleus. The nuclear Ca2+ store volume and release mechanism are clarified. By photostimulation, nuclear Ca2+ store can be released and impact the calcium in endoplasmic reticulum (ER), suggesting a Ca2+ transmission channel between nucleus and ER. The permeability of nuclear pore complex (NPC) to Ca2+ at different Ca2+ levels is also found different. This study indicates the existence of nuclear Ca2+ store and the final mapping of subcellular Ca2+ stores. This result thus is of great significance to the cell calcium theory, Ca2+ signaling, Ca2+-related cell processes, and further other Ca2+-related fields.