Despite the impressive success of metal halide perovskite nanocrystals (NCs) in diverse fields, such as solar cells, light-emitting diodes, photodetectors, and so forth, their intrinsic sensitivity to water limits the extending applications in aqueous systems. Herein, enhanced water stability is achieved for NH2-PEG-COOH capped Mn2+-doped CsPbCl3/CsPb2Cl5 core/shell NCs through the synergistic effect of ion doping, core/shell construction and polymer encapsulation. The NH2-PEG-COOH encapsulation is validated crucial for the formation of CsPbCl3/CsPb2Cl5 core/shell structure, since it retains contact for CsPbCl3 NCs with trace water, and guarantees a slow water-etching process, triggering the CsPbCl3 to CsPb2Cl5 transformation. Thanks to the high formation energy induced by Mn2+ doping, CsPbCl3/CsPb2Cl5 hetero core/shell construction and NH2-PEG-COOH protective barrier, the obtained NCs exhibit unattenuated photoluminescence quantum yield after dipped in water for 15 days. Based on the robust water stability, the NH2-PEG-COOH capped Mn2+-doped CsPbCl3/CsPb2Cl5 NCs work well in cell nucleus imaging and acid phosphatase detection. This work not only produces a novel perovskite fluorescence probe in aqueous systems but also provides a general and effective combination strategy to enhance the water stability of perovskite materials.