We present the first results of in situ atomic force microscope observation of the growth phenomena of trichosanthin (TCS) crystals. It is observed that the three-dimensional (3D) nucleation provides a dominant growth pathway on the cystal surface, with two kinds of characteristic features, scalelike and domelike nuclei. The scalelike nuclei appear to assemble in the <110> direction, while domelike nuclei demonstrate a much faster growth in the <1 (1) over bar0> direction. These particular growth phenomena are suggested to be determined by the unique molecular structures and interactions, according to the results of theoretical calculation. Along the <110> and <1 (1) over bar0> directions, molecules are arranged in away with their small domains binding the neighboring large domains, leading to strong hydrogen bonding between molecules. While along other directions, TCS molecules are associated with each other via weak van der Waals interactions. The diverse interactions along the different directions are responsible for the different binding behaviors of the molecules along different directions, which is further amplified as the selective assembling and asymmetry growth of (3D) nuclei along different directions.