Disclosed herein are a polymer nanocapsule and a preparing method thereof, and more particularly, a 3D covalent molecular network nanocapsule, and a preparing method thereof. According to the present invention, a nanocapsule having thermal stability and solvent resistance due to a 3D covalent molecular network structure may be easily prepared without performing an additional post-processing process such as addition of a cross-linking agent or catalyst or removal of a template or core. Since the nanocapsule formed as described above may support an organic dye, metal particles, and the like, it is expected that the nanocapsule will be variously applied to material storage and transport, drug delivery, and the like.