In this paper, we investigated the self-assembly and fractal feature of chitosan and Ag(I), Cu (II)-chitosan due to the theoretical and practical importance of chitosan in biomedical engineering, biomaterials and environmental sciences etc. The self-assembly and fractal structures of chitosan and Ag (I), Cu (II)-chitosan were observed using atomic force microscope (AFM), and the fractal dimensions of chitosan and Ag (I)- chitosan were calculated. The results indicate that their fractal dimension is approximate 2 and relates with the accumulation degree: the fractal dimension decreases with the accumulation degree increases. In addition, a new self-assembly strategy was presented to study the lyotropic liquid crystals (LLC) of chitosan and the formation mechanism of LLC was primarily analyzed and discussed. All of these results are valuable for the structure/function relationship study of chitosan and useful for application in biomedical materials.