The development of anti-water phosphorescent carbon dots (CDs) based materials is of great practical interest. Herein, we report a rational design of CDs based composite with anti-water phosphorescence by controlling a one-step microwave assisted heating of green fluorescent CDs and urea. Upon increasing the microwave-heating temperature, urea was gradually converted to CN, in which the CDs were uniformly embedded in the CN matrix. The fluorescence/phosphorescence intensity of these CDs based composites are determined by the morphologies of the CN, which can be adjusted by controlling the microwave heating time. More importantly, the combining CDs in CN not only promote the phosphorescence emission but also prevent the phosphorescence quenching by water, leading to stable phosphorescence emission in aqueous environment. Based on the anti-water phosphorescence properties of these CDs based composites, a concept of multiple data encryption was demonstrated.