The invention belongs to the technical field of nanometer material preparation, and relates to a preparation method of chitosan nanoparticles, in particular to a preparation method and an application of the chitosan nanoparticles with pore structures. According to the preparation method and the application of the chitosan nanoparticles with the pore structures, first, chitosan is dissolved into acetic acid solution, and chitosan solution is obtained; second, span-80 is dissolved into organic solvent to obtain oil phase, third, the chitosan solution and the oil phase is cut and emulsified in a high speed, and opposite phase miniemulsion is obtained; the opposite phase miniemulsion is stirred and cross linker solution is dropped into the opposite phase miniemulsion to react; and then a system is decompressed, dehydrated, centrifugated, washed and vacuum dryed, so that the chitosan nanoparticles with the pore structures are obtained. According to the preparation method and the application of the chitosan nanoparticles with the pore structures, the grain diameters of the chitosan nanoparticles with the pore structures are ranged from 100 nm - 500 nm, and the chitisan nanoparticles with the pore structures are good carriers of medicines, and can be used for medicine absorption. Meanwhile, in preparation process, water phase and the oil phase inside the opposite phase miniemulsion are similar, so that the production efficiency of nanoparticles is high.