We report here a study on the microstructure formation process of polymeric nanoparticles based on polyelectrolyte complexes. When polyanion poly(acrylic acid) (PAA) was dropped into polycation chitosan (CS) solution, CS-PAA nanoparticles with diverse microstructure would be formed under different experimental conditions. The microstructure of CS-PAA nanoparticles changed from solid spherical nanoparticles to core-shell separative ones and turned back to solid spherical ones with the variation of preparation conditions. The influence of molecular weight of CS and PAA, shell cross-linking, dropping temperature on the size, stability and morphology of CS-PAA nanoparticles were also studied. The nanoparticle size was affected by the molecular weight of CS and PAA, the ratio of amino group to carboxyl group (na/nc) and the incubation temperature as well. The shell-cross-linking provides a means to stabilize these nanoparticles. These nanoparticles can encapsulate plasmid DNA very well, which makes them have great potential in gene delivery.