Self-assembled structures of three dimethyl isophthalate-functionalized Janus dendrimers G(1)G(2)COOCH(3), G(0)G(3)COOCH(3), and G(1)G(3)COOCH(3) were investigated with scanning tunneling microscopy (STM) on HOPG. It was found that G(1)G(2)COOCH(3), G(0)G(3)COOCH(3), G(1)G(3)COOCH(3) assembled into ordered, partial ordered, and disordered structures, respectively. After heated to 60-80 degrees C, regular dendrimer dimers, could be found on HOPG, resulting in close-packed ordered structures instead of the previous disordered structures. The results show that with the increase of the molecule generation, molecules are bound down onto surface due to the enhanced intermolecular and molecule-substrate interactions. The self-assembly is dependent on the dynamic process, leading to disordered structures. However, when heated, the mobility of dendrimer molecules on surface could be improved. Structural transformation from disordered structures to thermodynamically stable dimeric structures could be observed by STM on G(0)G(3)COOCH(3) and G(1)G(3)COOCH(3) adlayers.