The assembling structure of square and triangular macrocycle molecules constructed with diethynylcarbazole units was investigated by scanning tunneling microscopy (STM) on a graphite surface. STM observation revealed that the square macrocycle molecule (M1) forms a multilayer on the graphite surface. In the first layer, M1 assembles into medium-sized domains with a few defects and dislocations, whereas, for the second layer, most of M1 are dispersed on the first layer separately. A tentative stacking mode of the bilayer structure is provided in this paper on the basis of information given by STM experiments. Considering the interlayer distance given by the crystal data on the similar molecules and the length of the M1 alkyl chains, we think that it is possible that part of the top M1 side chains adsorbs on the cavity area of the bottom M1 and probably plays a dominant role in stabilizing the second layer. This postulation is verified by a control experiment in which coronene is filled in the cavity of M1 and no bilayer structure of M1 is found. The triangular molecule (M2) organizes into a single layer with larger and less defect domains. Two M2 are paired together in parallel, but opposite-oriented style, and are responsible for the serrate edge of the molecular row. The alkyl chains of M2 adopt rather diverse arrangements without disturbing the assembly of M2 core parts. When the solution contains both coronene and M2, no M2–coronene complex is observed and the adlayer characteristics of M2 are essentially the same as those of only M2 in solution. The results may help us to learn the stacking behavior of macrocycle molecules with different shapes, understand surface self-assembling principles, and develop high-performance devices based on related materials.